Title of Invention

"DOUBLE STRANDED OLIGONUCLEOTIDE INHIBITORS OF RTP801"

Abstract A compound having the double-stranded structure: wherein each N and N' is a ribonucleotide which may be modified or unmodified in its sugar residue and each of (N)x and (N')y is an oligomer in which each consecutive N or N' is joined to the next N or N' by a covalent bond; wherein each of x and y is an integer between 19 and 40 inclusive; wherein each of Z and Z' may be present or absent, but if present is dTdT and is covalently attached at the 3' terminus of the strand in which it is present; and wherein the sequence of (N)x comprises a first stretch of contiguous nucleotides having any one of the following sequences: AGCUGCAUCAGGUUGGCAC (SEQ ID NO:66); UUCUAGAUGGAAGACCCAG (SEQ ID NO:74); UUGAACAUCAAGUGUAUUC (SEQ ID NO:75); AAAAAUAUUGCAUAGGUCU (SEQ ID NO:77); UACUUGAACAUCAAGUGUA (SEQ ID NO:79); and AACUCAAUGAGCUUCCUGG (SEQ ID NO:91); and the sequence of (N')y comprises a second stretch of contiguous nucleotides, and wherein the double-stranded structure is generated by base-pairing between the first stretch and the second stretch.
Full Text The present invention relates to double stranded oligonucleotide inhibitors of RTP801.
This application claims priority of EP patent application No. EP 04019405.2, filed 16 August 2004; US provisional applications Nos. 60/601,983, filed 17 August 2004; 60/604,668, filed 25 August 2004; 60/609,786, filed 14 September 2004; 60/638,659, filed 22 December 2004; 60/664,236, filed 22 March 2005 and 60/688,943, filed 8 June 2005, all of which are hereby incorporated by reference in their entirety.
FIELD OF THE INVENTION
The present invention relates to novel siRNA molecules which inhibit the RTP801 gene and to the use of such molecules to treat respiratory disorders of all types (including pulmonary disorders), eye diseases and conditions, microvascular disorders, angiogenesis- and apoptosis-related conditions.
BACKGROUND OF THE INVENTION
Chronic obstructive pulmonary disease (COPD)
Chronic obstructive pulmonary disease (COPD), affects more than 16 million Americans and is the fourth highest cause of death in the United States. Cigarette smoking causes most occurrences of the debilitating disease but other environmental factors cannot be excluded (Petty TL. 2003. Definition, epidemiology, course, and prognosis of COPD. Clin. Cornerstone, 5-10).
Pulmonary emphysema is a major manifestation of COPD. Permanent destruction of peripheral air spaces, distal to terminal bronchioles, is the hallmark of emphysema (Tuder RM.et al . Oxidative stress and apoptosis interact and cause emphysema due to vascular endothelial growth factor blocade. Am J Respir Cell Mol Biol, 29:88-97; 2003.). Emphysema is also characterized by accumulation of inflammatory cells such as macrophages and neutrophils in bronchioles and alveolar structures (Petty, 2003).
The pathogenesis of emphysema is complex and multifactorial. In humans, a deficiency of inhibitors of proteases produced by inflammatory cells, such as alpha 1-antitrypsin, has been
shown to contribute to protease/antiprotease imbalance, thereby favoring destruction of alveolar
extracellular matrix in cigarette-smoke (CS) induced emphysema (Eriksson, S. 1964. Pulmonary
Emphysema and Alpha]-AntiIrypsin Deficiency. Ada Med Scand 175:197-205. Joos, L., Pare,
P.D., and Sandford, A.J. 2002. Genetic risk factors of chronic obstructive pulmonary disease.
Swiss Med Wkly 7J2.27-37). Matrix metalloproteinases (MMPs) play a central role in
experimental emphysema, as documented by resistance of macrophage metalloelastase knockout
mice against emphysema caused by chronic inhalation of CS (Hautamaki, et al: Requirement for
macrophage elastasefor cigarette smoke-induced emphysema in mice. Science 277:2002-2004).
Moreover, pulmonary overexpression of interleukin-13 in transgenic mice results in MMP- and
cathepsin-dependent emphysema (Zheng, T., et al 2000. Inducible targeting oflL-13 to the adult
lung causes matrix metalloproteinase- and cathepsin-dependent emphysema. J Clin Invest
106:1081-1093). Recent works describe involvement of septal cell apoptosis in lung tissue
destruction leading to emphysema (Rangasami T, et al . Genetic ablation of Nrf2 enhances
susceptibility to cigarette smoke-iduced emphysema in mice. Submitted to Journal ofClinincal
Investigation.; Tuder RM et al. Oxidative stress and apoptosis interact and cause emphysema
due to vascular endothelial growth factor blocade. AmJRespir Cell Mol Biol, 29:88-97; 2003.;
Yokohori N, Aoshiba K, Nagai A, Increased levels of cell death and proliferation in alveolar
wall cells in patients with pulmonary emphysema. Chest. 2004 Feb;125(2):626-32.\ Aoshiba K,
Yokohori N, Nagai A., Alveolar wall apoptosis causes lung destruction and emphysematous
changes. Am J Respir Cell Mol Biol. 2003 May;28(5):555-62.).
Among the mechanisms that underlie both pathways of lung destruction in emphysema,
excessive formation of reactive oxygen species (ROS) should be first of all mentioned. It is well
established that prooxidant/antioxidant imbalance exists in the blood and in the lung tissue of
smokers (Hulea SA, et al: Cigarette smoking causes biochemical changes in blood that are
suggestive ofoxidative stress: a case-control study. J Environ Pat hoi Toxicol Oncol. 1995; 14(3-
4): 173-80.; Rahman I, MacNee W. Lung glutathione and oxidative stress: implications in
cigarette smoke-induced airway disease. Am J Physiol. 1999 Dec;277(6 Pt l):L1067-88.;
MacNee W. Oxidants/antioxidants and COPD. Chest. 2000 May;117(5 Suppl 1):303S-17S.;
Marwick JA, Kirkham P, Gilmour PS, Donaldson K, MacNEE W, Rahman I. Cigarette smokeinduced
oxidative stress and TGF-betal increase p21\vafl/cipl expression in alveolar epithelial
cells. Ann N YAcadSci. 2002 Nov;973:278-83.; Aoshiba K, Koinuma M, Yokohori N, Nagai A.
Immunohistochemical evaluation of oxidative stress in murine lungs after cigarette smoke
exposure. Inhal Toxicol. 2003 Sep; 15(10): 1029-38.; Dekhuijzen PN. Antioxidanl properties of
N-acetylcysteine: their relevance in relation to chronic obstructive pulmonary disease. Eur
Respir J. 2004 Apr;23(4):629-36.; Tuder RM, Zhen L, Cho CY, Taraseviciene-Stewart L,
Kasahara Y, Salvemini D, Voelkel NF, and Flores SC. Oxidative stress and apoptosis interact
and cause emphysema due to vascular endothelial growth factor blocade. Am J Respir Cell Mol
Biol, 29:88-97; 2003.). After one hour exposure of mice to CS, there is a dramatic increase of 8-
hydroxy-2'-deoxyguanosine (8-OHdG) in the alveolar epithelial cells, particularly of type II (see
Inhal Toxicol. 2003 Sep; 15(10):! 029-3 8. above).
Overproduced reactive oxygen species are known for their cytotoxic activity, which stems from
a direct DNA damaging effect and from the activation of apoptotic signal transduction pathways
(Takahashi A, Masuda A, Sun M, Centonze VE, Herman B. Oxidative stress-induced apoptosis
is associated with alterations in mitochondrial caspase activity and Bcl-2-dependent alterations
in mitochondrial pH (pHm). Brain Res Bull. 2004 Feb 15;62(6):497-504.; Taniyama Y,
Griendling KJC. Reactive oxygen species in the vasculature: molecular and cellular
mechanisms. Hypertension. 2003 Dec;42(6): 1075-81. Epub 2003 Oct 27.; Higuchi Y.
Chromosomal DNA fragmentation in apoptosis and necrosis induced by oxidative stress.
Biochem Pharmacol. 2003 Oct 15;66(8):1527-35.; Punj V, Chakrabarty AM. Redoxproteins in
mammalian cell death: an evolutionary conserved function in mitochondria and prokaryotes.
Cell Microbiol. 2003 Apr;5(4):225-31.; Ueda S, Masutani H, Nakamura H, Tanaka T, Ueno M,
Yodoi J. Redox control of cell death. Antioxid Redox Signal. 2002 Jun;4(3):405-14.).
ROS's are not only cytotoxic per se but are also proinflammatory stimuli, being prominent
activators of redox-sensitive transcription factors NFkB and AP-1 (reviewed in Rahman I.
Oxidative stress and gene transcription in asthma and chronic obstructive pulmonary disease:
antioxidant therapeutic targets. Curr Drug Targets Inflamm Allergy. 2002 Sep;l(3):291-315.).
Both transcription factors are, in turn, strongly implicated in stimulation of transcription of
proinflammatory cytokines (reviewed in Renard P, Raes M. The proinflammatory transcription
factor NFkappaB: a potential target for novel therapeutical strategies. Cell Biol Toxicol.
!999;15(6):341-4.; Lentsch AB, Ward PA. The NFkappaBb/IkappaB system in acute
inflammation. Arch Immunol Ther Exp (Warsz). 2000;48(2):59-63) and matrix degrading
proteinases (Andela VB, Gordon AH, Zotalis G, Rosier RN, Goater JJ, Lewis GD, Schwarz EM,
Puzas JE, O'Keefe RJ. NFkappaB: a pivotal transcription factor in prostate cancer metastasis to
bone. Clin Orthop. 2003 Oct;(415 Suppl):S75-85.; Fleenor DL, Pang IH, Clark AF. Involvement
of AP-1 in interleukin-1 alpha-stimulated MMP-3 expression in human trabecular meshwork
cells. Invest Ophthalmol VisSci. 2003 Aug;44(8):3494-501.; Ruhul Amin AR, Senga T, Oo ML,
Thant AA, Hamaguchi M. Secretion of matrix metalloproteinase-9 by the proinflammatory
cytokine, IL-lbeta: a role for the dual signalling pathways, Akt and Erk. Genes Cells. 2003
Jun;8(6):515-23.). Proinflammatory cytokines, in turn, serve as attractors of inflammatory cells
that also secrete matrix degrading enzymes, cytokines and reactive oxygen species. Thus, it
appears that a pathogenic factor, like e.g. CS, triggers a pathological network where reactive
oxygen species act as major mediators of lung destruction.
Both reactive oxygen species (ROS) from inhaled cigarette smoke and those endogenously
formed by inflammatory cells contribute to an increased intrapulmonary oxidant burden.
One additional pathogenic factor with regards to COPD pathogenesis is the observed decreased
expression of VEGF and VEGFRII in lungs of emphysematous patients (Yasunori Kasahara,
Rubin M. Tuder, Carlyne D. Cool, David A. Lynch, Sonia C. Flores, and Norbert F. Voelkel.
Endothelial Cell Death and Decreased Expression of Vascular Endothelial Growth Factor and
Vascular Endothelial Growth Factor Receptor 2 in Emphysema. AmJRespir Crit Care Med Vol
163. pp 737-744, 200 J). Moreover, inhibition of VEGF signaling using chemical VEGFR
inhibitor leads to alveolar septal endothelial and then to epithelial cell apoptosis, probably due to
disruption of intimate structural/functional connection of both types of cells within alveoli
(Yasunori Kasahara, Rubin M. Tuder, Laimute Taraseviciene-Stewart, Timothy D. Le Cras,
Steven Abman, Peter K. Hirth, Johannes Waltenberger, and Norbert F. Voelkel. Inhibition of
VEGF receptors causes lung cell apoptosis and emphysema. J. Clin. Invest. 106:1311-1319
(2000).; Voelkel NF, Cool CD. Pulmonary vascular involvement in chronic obstructive
pulmonary disease. Eur Respir JSuppl. 2003 Nov;46:28s-32s).
Macular degeneration
The most common cause of decreased best-corrected vision in individuals over 65 years of age
in the US is the retinal disorder known as age-related macular degeneration (AMD). As AMD
progresses, the disease is characterized by loss of sharp, central vision. The area of the eye
affected by AMD is the Macula - a small area in the center of the retina, composed primarily of
photoreceptor cells. So-called "dry" AMD, accounting for about 85% - 90% of AMD patients,
involves alterations in eye pigment distribution, loss of photoreceptors and diminished retinal
function due to overall atrophy of cells. So-called "wet" AMD involves proliferation of
abnormal choroidal vessels leading to clots or scars in the sub-retinal space. Thus, the onset of
wet AMD occurs because of the formation of an abnormal choroidal neovascular network
(choroidal neovascularization, CNV) beneath the neural retina. The newly formed blood vessels
are excessively leaky. This leads to accumulation of subretinal fluid and blood leading to loss of
visual acuity. Eventually, there is total loss of functional retina in the involved region, as a large
disciform scar involving choroids and retina forms. While dry AMD patients may retain vision
of decreased quality, wet AMD often results in blindness. (Hamdi & Kenney, Age-related
Macular degeneration - a neve viewpoint, Frontiers in Bioscience, e305-314, May 2003). CNV
occurs not only in wet AMD but also in other ocular pathologies such as ocular histoplasmosis
syndrome, angiod streaks, ruptures in Bruch's membrane, myopic degeneration, ocular tumors
and some retinal degenerative diseases.
Various studies conducted have determined several risk factors for AMD, such as smoking,
aging, family history (Milton, Am J Ophthalmol 88, 269 (1979); Mitchell et al., Ophthalmology
102, 1450-1460 (1995); Smith et al., Ophthalmology 108, 697-704 (2001)) sex (7-fold higher
likelihood in females: Klein et al., Ophthalmology 99, 933-943 (1992) and race (whites are most
susceptible). Additional risk factors may include eye characteristics such as farsightedness
(hyperopia) and light-colored eyes, as well as cardiovascular disease and hypertension.
Evidence of genetic involvement in the onset progression of the disease has also been
documented (see Hamdi & Kenney above).
Two companies, Acuity Pharmaceuticals and Sirna Therapeutics, have both recently filed an
IND for siRNA molecules inhibiting VEGF and VEGF-R1 (Flt-1), respectively, for treatment of
AMD. These molecules are termed Cand5 inhibitor and 027 inhibitor respectively.
Microvascular disorders
Microvascular disorders are composed of a broad group of conditions that primarily affect the
microscopic capillaries and lymphatics and are therefore outside the scope of direct surgical
intervention. Microvascular disease can be broadly grouped into the vasospastic. the yasculitis
and lymphatic occlusive. Additionally, many of the known vascular conditions have a
microvascular element to them.
• Vasospastic Disease - Vasospastic diseases are a group of relatively common conditions
where, for unknown reasons, the peripheral vasoconstrictive reflexes are hypersensitive.
This results in inappropriate vasoconstriction and tissue ischaemia, even to the point of
tissue loss. Vasospastic symptoms are usually related to temperature or the use of
vibrating machinery but may be secondary to other conditions.
• Vasculitic Disease - Vasculitic diseases are those that involve a primary inflammatory
process in the microcirculation. Vasculitis is usually a component of an autoimmune or
connective tissue disorder and is not generally amenable to surgical treatment but
requires immunosuppressive treatment if the symptoms are severe.
• Lymphatic Occlusive Disease - Chronic swelling of the lower or upper limb
(lymphoedema) is the result of peripheral lymphatic occlusion. This is a relatively rare
condition that has a large number of causes, some inherited, some acquired. The
mainstays of treatment are correctly fitted compression garments and the use of
intermittent compression devices.
Microvascular pathologies associated with diabetes
Diabetes is the leading cause of blindness, the number one cause of amputations and impotence,
and one of the most frequently occurring chronic childhood diseases. Diabetes is also the
leading cause of end-stage renal disease in the United States, with a prevalence rate of 31%
compared with other renal diseases. Diabetes is also the most frequent indication for kidney
transplantation, accounting for 22% of all transplantation operations.
In general, diabetic complications can be classified broadly as microvascular or macrovascular
disease. Microvascular complications include neuropathy (nerve damage), nephropathy (kidney
disease) and vision disorders (eg retinopathy, glaucoma, cataract and corneal disease). In the
retina, glomerulus, and vasa nervorum, similar pathophysiologic features characterize diabetesspecific
microvascular disease.
Microvascular pathologies associated with diabetes are defined as a disease of the smallest
blood vessels (capillaries) that may occur e.g. in people who have had diabetes for a long time.
The walls of the vessels become abnormally thick but weak. They, therefore, bleed, leak protein
and slow the flow of blood through the body.
Clinical and animal model data indicate that chronic hyperglycemia is the central initiating
factor for all types of diabetic microvascular disease. Duration and magnitude of hyperglycemia
are both strongly correlated with the extent and rate of progression of diabetic microvascular
disease. Although all diabetic cells are exposed to elevated levels of plasma glucose,
hyperglycemic damage is limited to those cell types (e.g., endothelia] cells) that develop
intracellular hyperglycemia. Endothelial cells develop intracellular hyperglycemia because,
unlike many other cells, they cannot down-regulate glucose transport when exposed to
extracellular hyperglycemia. That intracellular hyperglycemia is necessary and sufficient for the
development of diabetic pathology is further demonstrated by the fact that overexpression of the
GLUT1 glucose transporter in mesangial cells cultured in a normal glucose milieu mimics the
diabetic phenotype, inducing the same increases in collagen type IV, collagen type I, and
fibronectin gene expression as diabetic hyperglycemia.
Abnormal Endothelial Cell Function; Early in the course of diabetes mellitus, before structural
changes are evident, hyperglycemia causes abnormalities in blood flow and vascular
permeability in the retina, glomerulus, and peripheral nerve vasa nervorum. The increase in
blood flow and intracapillary pressure is thought to reflect hyperglycemia-induced decreased
nitric oxide (NO) production on the efferent side of capillary beds, and possibly an increased
sensitivity to angiotensin II. As a consequence of increased intracapillary pressure and
endothelial cell dysfunction, retinal capillaries exhibit increased leakage of fluorescein and
glomerular capillaries have an elevated albumin excretion rate (AER). Comparable changes
occur in the vasa vasorum of peripheral nerve. Early in the course of diabetes, increased
permeability is reversible; as time progresses, however, it becomes irreversible.
Increased Vessel Wall Protein Accumulation
The common pathophysiologic feature of diabetic microvascular disease is progressive
narrowing and eventual occlusion of vascular lumina, which results in inadequate perfusion and
function of the affected tissues. Early hyperglycemia-induced microvascular hypertension and
increased vascular permeability contribute to irreversible microvessel occlusion by three
processes:
" The first is an abnormal leakage of periodic acid-Schiff (PAS)-positive, carbohydratecontaining
plasma proteins, which are deposited in the capillary wall and which may
stimulate perivascular cells such as pericytes and mesangial cells to elaborate growth
factors and extracellular matrix.
* The second is extravasation of growth factors, such as transforming growth factor pi
(TGF-P1), which directly stimulates overproduction of extracellular matrix components,
and may induce apoptosis in certain complication-relevant cell types.
" The third is hypertension-induced stimulation of pathologic gene expression by
endothelial cells and supporting cells, which include glut-1 glucose transporters, growth
factors, growth factor receptors, extracellular matrix components, and adhesion
molecules that can activate circulating leukocytes. The observation that unilateral
reduction in the severity of diabetic microvascular disease occurs on the side with
ophthalmic or renal artery stenosis is consistent with this concept.
Microvascular Cell Loss and Vessel Occlusion
The progressive narrowing and occlusion of diabetic microvascular lumina are also
accompanied by microvascular cell loss. In the retina, diabetes mellirus induces programmed
cell death of Miiller cells and ganglion cells, pericytes, and endothelial cells. In the glomerulus,
declining renal function is associated with widespread capillary occlusion and podocyte loss, but
the mechanisms underlying glomerular cell loss are not yet known. In the vasa nervorum,
endothelial cell and pericyte degeneration occur, and these microvascular changes appear to
precede the development of diabetic peripheral neuropathy. The multifocal distribution of
axonal degeneration in diabetes supports a causal role for microvascular occlusion, but
hyperglycemia-induced decreases in neurotrophins may contribute by preventing normal axonal
repair and regeneration.
Another common feature of diabetic microvascular disease has been termed hyperglycemic
memory, or the persistence or progression of hyperglycemia-induced microvascular alterations
during subsequent periods of normal glucose homeostasis. The most striking example of this
phenomenon is the development of severe retinopathy in histologically normal eyes of diabetic
dogs that occurred entirely during a 2.5-year period of normalized blood glucose that followed
2.5 years of hyperglycemia. Hyperglycemia-induced increases in selected matrix gene
transcription also persist for weeks after restoration of normoglycemia in vivo, and a less
pronounced, but qualitatively similar, prolongation of hyperglycemia-induced increase in
selected matrix gene transcription occurs in cultured endothelial cells.
For further information, see "Shared pathophysiologic features of microvascular complications
of diabetes" (Larsen: Williams Textbook of Endocrinology, 10th ed., Copyright © 2003
Elsevier).
Microvascular complications occur not only in overt diabetes but are also due to Impaired
Glucose Tolerance (IGT). Microvascular complications of IGT: neuropathy, retinopathy, and
renal microproteinuria.
Diabetic neuropathy
Diabetic neuropathies are neuropathic disorders (peripheral nerve damage) that are associated
with diabetes mellitus. These conditions usually result from diabetic microvascular injury
involving small blood vessels that supply nerves (vasa nervorum). Relatively common
conditions which may be associated with diabetic neuropathy include third nerve palsy;
mononeuropathy; mononeuropathy multiplex; diabetic amyotrophy; a painful polyneuropathy;
autonomic neuropathy; and thoracoabdominal neuropathy and the most common form,
peripheral neuropathy, which mainly affects the feet and legs. There are four factors involved in
the development of diabetic neuropathy: microvascular disease, advanced glycated end
products, protein kinase C, and the polyol pathway.
Microvascular disease in diabetic neuropathy
Vascular and neural diseases are closely related and intertwined. Blood vessels depend on
normal nerve function, and nerves depends on adequate blood flow. The first pathological
change in the microvasculature is vasoconstriction. As the disease progresses, neuronal
dysfunction correlates closely with the development of vascular abnormalities, such as capillary
basement membrane thickening and endothelial hyperplasia, which contribute to diminished
oxygen tension and hypoxia. Neuronal ischemia is a well-established characteristic of diabetic
neuropathy. Vasodilator agents (e.g., angiotensin-converting-enzyme inhibitors, alphalantagonists)
can lead to substantial improvements in neuronal blood flow, with corresponding
improvements in nerve conduction velocities. Thus, microvascular dysfunction occurs early in
diabetes, parallels the progression of neural dysfunction, and may be sufficient to support the
severity of structural, functional, and clinical changes observed in diabetic neuropathy.
Peripheral neuropathy (legs), sensorimotor neuropathy is a significant component in the
pathogenesis of leg ulcers in diabetes.
Neuropathy is a common complication of diabetes occurring over time in more than half of
patients with type 2 diabetes. Nerve conduction studies demonstrate that neuropathy is already
present in 10-18% of patients at the time of diabetes diagnosis, suggesting that peripheral nerve
injury occurs at early stages of disease and with milder glycemic dysregulation. The concept
that neuropathy is an early clinical sign of diabetes was proposed >40 years ago, and most
studies report an association between IGT and neuropathy. Most patients with IGT and
associated neuropathy have a symmetric, distal sensory polyneuropathy with prominent
neuropathic pain. IGT neuropathy (Microvascular complications of impaired glucose tolerance
- Perspectives in Diabetes, J. Robinson Singleton, in Diabetes December 1, 2003) is
phenotypically similar to early diabetic neuropathy, which also causes sensory symptoms,
including pain, and autonomic dysfunction. In a survey of 669 patients with early diabetic
neuropathy, sensory symptoms were present in >60%, impotence in nearly 40%, and other
autonomic involvement in 33%, but evidence of motor involvement in only 12%. These clinical
findings suggest prominent early involvement of the small unmyelinated nerve fibers that carry
pain, temperature, and autonomic signals. Direct quantitation of unmyelinated intraepidermal
nerve fibers from skin biopsies shows similar fiber loss and altered morphology in patients with
neuropathy associated with IGT and early diabetes .
Autonomic dysfunction, particularly erectile dysfunction and altered cardiac vagal response, are
common early features of neuropathic injury in diabetes. Work with IGT patients also suggests
prevalent vagal dysautonoinia: separate studies have found abnormal heart rate recovery
following exercise, blunted R-R interval variability to deep breathing, and reduced expiration to
inspiration ratio (all measures of vagal dysautonomia) in a greater fraction of IGT patients than
age-matched normoglycemic control subjects.
Nerve damage in diabetes affects the motor, sensory, and autonomic fibers. Motor neuropathy
causes muscle weakness, atrophy, and paresis. Sensory neuropathy leads to loss of the protective
sensations of pain, pressure, and heat. The absence of pain leads to many problems in the
insensate foot, including ulceration, unperceived trauma, and Charcot neuroarthropathy. The
patient may not seek treatment until after the wound has advanced. A combination of sensory
and motor dysfunction can cause the patient to place abnormal stresses on the foot, resulting in
trauma, which may lead to infection. Autonomic sympathetic neuropathy causes vasodilation
and decreased sweating, which results in warm, overly dry feet that are particularly prone to
skin breakdown, as well as functional alterations in microvascular flow. Autonomic dysfunction
(and denervation of dermal structures) also results in loss of skin integrity, which provides an
ideal site for microbial invasion. The neuropathic foot does not ulcerate spontaneously; rather, it
is the combination of some form of trauma accompanied by neuropathy.
Microvascular dysfunction occurs early in diabetes, parallels the progression of neural
dysfunction, and may be sufficient to support the severity of structural, functional, and clinical
changes observed in diabetic neuropathy.
Advanced glycated end products - Elevated intracellular levels of glucose cause a nonenzymatic
covalent bonding with proteins, which alters their structure and destroys their
function. Certain of these glycated proteins are implicated in the pathology of diabetic
neuropathy and other long term complications of diabetes.
Protein kinase C (PKC) - PKC is implicated in the pathology of diabetic neuropathy. Increased
levels of glucose cause an increase in intracellular diacylglycerol, which activates PKC. PKC
inhibitors in animal models will increase nerve conduction velocity by increasing neuronal
blood flow.
Sensorimotor polyneuropathy
Longer nerve fibers are affected to a greater degree than shorter ones, because nerve conduction
velocity is slowed in proportion to a nerve's length. In this syndrome, decreased sensation and
loss of reflexes occurs first in the toes bilaterally, then extends upward. It is usually described as
glove-stocking distribution of numbness, sensory loss, dysesthesia and nighttime pain. The pain
can feel like burning, pricking sensation, achy or dull. Pins and needles sensation is common.
Loss of proprioception, that is, the sense of where a limb is in space, is affected early. These
patients cannot feel when they are stepping on a foreign body, like a splinter, or when they are
developing a callous from an ill-fitting shoe. Consequently, they are at risk for developing ulcers
and infections on the feet and legs, which can lead to amputation. Similarly, these patients can
get multiple fractures of the knee, ankle or foot, and develop a Charcot joint. Loss of motor
function results on dorsiflexion contractures of the toes, so called hammertoes. These
contractures occur not only in the foot but also in the hand.
Autonomic neuropathy
The autonomic nervous system is composed of nerves serving the heart, GI tract and urinary
system. Autonomic neuropathy can affect any of these organ systems. The most commonly
recognized autonomic dysfuction in diabetics is orthostatic hypotension, or the uncomfortable
sensation of fainting when a patient stands up. In the case of diabetic autonomic neuropathy, it is
due to the failure of the heart and arteries to appropriately adjust heart rate and vascular tone to
keep blood continually and fully flowing to the brain. This symptom is usually accompanied by
a loss of sinus respiratory variation, that is, the usual change in heart rate seen with normal
breathing. When these two findings are present, cardiac autonomic neuropathy is present.
GI tract manifestations include delayed gastric emptying, gastroparesis, nausea, bloating, and
diarrhea. Because many diabetics take oral medication for their diabetes, absorption of these
medicines is greatly affected by the delayed gastric emptying. This can lead to hypoglycemia
when an oral diabetic agent is taken before a meal and does not get absorbed until hours, or
sometimes days later, when there is normal or low blood sugar already. Sluggish movement of
the small instestine can cause bacterial overgrowth, made worse by the presence of
hyperglycemia. This leads to bloating, gas and diarrhea.
Urinary symptoms include urinary frequency, urgency, incontinence and retention. Again,
because of the retention of sweet urine, urinary tract infections are frequent. Urinary retention
can lead to bladder diverticula, stones, reflux nephropathy.
Cranial neuropathy
When cranial nerves are affected, oculomotor (3rd) neuropathies are most common. The
oculomotor nerve controls all of the muscles that move the eye with the exception of the lateral
rectus and superior oblique muscles. It also serves to constrict the pupil and open the eyelid. The
onset of a diabetic third nerve palsy is usually abrupt, beginning with frontal or periorbital pain
and then diplopia. All of the oculomotor muscles innervated by the third nerve may be affected,
except for those that control pupil size. The sixth nerve, the abducens nerve, which innervates
the lateral rectus muscle of the eye (moves the eye laterally), is also commonly affected but
fourth nerve, the trochlear nerve, (innervates the superior oblique muscle, which moves the eye
downward) involvement is unusual. Mononeuropathies of the thoracic or lumbar spinal nerves
can occur and lead to painful syndromes that mimic myocardial infarction, cholecystitis or
appendicitis. Diabetics have a higher incidence of entrapment neuropathies, such as carpal
tunnel syndrome.
Diabetic Limb Ischemia and Diabetic foot ulcers
Diabetes and pressure can impair microvascular circulation and lead to changes in the skin on
the lower extremities, which in turn, can lead to formation of ulcers and subsequent infection.
Microvascular changes lead to limb muscle microangiopathy, as well as a predisposition to
develop peripheral ischemia and a reduced angiogenesis compensatory response to ischemic
events. Microvascular pathology exacerbates Peripheral Vascular Disease (PVD) (or Peripheral
Arterial Disease (PAD) or Lower Extremity Arterial Disease (LEAD)- a MACROvascular
complication - narrowing of the arteries in the legs due to atherosclerosis. PVD occurs earlier in
diabetics, is more severe and widespread, and often involves intercurrent microcirculatory
problems affecting the legs, eyes, and kidneys.
Foot ulcers and gangrene are frequent comorbid conditions of PAD. Concurrent peripheral
neuropathy with impaired sensation make the foot susceptible to trauma, ulceration, and
infection. The progression of PAD in diabetes is compounded by such comorbidity as peripheral
neuropathy and insensitivity of the feet and lower extremities to pain and trauma. With impaired
circulation and impaired sensation, ulceration and infection occur. Progression to osteomyelitis
and gangrene may necessitate amputation.
Persons with diabetes are up to 25 times more likely than nondiabetic persons to sustain a lower
limb amputation, underscoring the need to prevent foot ulcers and subsequent limb loss.
Diabetic foot ulcers may occur not only in conjunction with PAD but may also be associated
with neuropathy, venous insufficiency (varicose veins), trauma, and infection. PAD contributes
to these other conditions in producing or precipitating foot ulcers. Foot ulcers do not necessarily
represent progression of PAD, as they may occur in the presence of adequate clinical peripheral
arterial perfusion. Patient- based studies indicate an increased risk of foot ulceration in diabetic
patients who have peripheral neuropathy and a high plantar foot pressure. The prevalence of a
history of ulcers or sores on the foot or ankles was 15% of all diabetic patients in the populationbased
study in southern Wisconsin. The prevalence was higher for diabetic individuals
diagnosed at age greater in insulin-treated diabetic patients (17%) than in patients not taking insulin (10%). The
prevalence increased with age, especially in diabetic patients diagnosed at age patient studies from Europe, prevalence of foot ulcers in diabetic patients was 3% in those age
in males than in females at age 70 years.
15
In diabetic patients, foot ischemia and infection are serious and even life-threatening
occurrences; however, neuropathy is the most difficult condition to treat . The medical and
surgical literature concerning all aspects of the clinical and pathological manifestations of the
diabetic foot is overwhelming. Neuropathy, angiopathy, retinopathy, and nephropathy, alone or
in combination and in varying degrees of severity, may influence the treatment of the diabetic
foot.
Every year, 82,000 limb amputations are performed in patients with diabetes mellitus. The
majority of these amputations are performed in the elderly population. Amputations resulting
from diabetes may arise from multiple etiologies, including foot ulcers, ischemia, venous leg
ulcers (ie, those secondary to venous reflux), and heel ulcers (ie, those resulting from untreated
pressure ulcers in the heel). The majority of these amputations originate from ulcers. The
prevalence of foot ulcers among patients with diabetes is 12%. In addition, the 20-year
cumulative incidence of lower-extremity ulcers in patients with type 1 diabetes is 9.9%.
Diabetes-induced limb amputations result in a 5-year mortality rate of 39% to 68% and are
associated with an increased risk of additional amputations. The length of hospital stay is
approximately 60% longer among patients with diabetic foot ulcers, as compared with those
without ulcers.
Diabetic neuropathy impairs the nerve axon reflex that depends on healthy C-fiber nociceptor
function and causes local vasodilation in response to a painful stimulus. This condition further
compromises the vasodilatory response present in conditions of stress, such as injury or
inflammation, in the diabetic neuropathic foot. This impairment may partially explain why some
ulcers in the diabetic neuropathic foot are either slow to heal or fail to heal at all, despite
successful lower-extremity revascularization.
The most common causal pathway to diabetic foot ulceration can thus be identified as the
combination of neuropathy (sensory loss), deformity (eg, prominent metatarsal heads), arid
trauma (eg, ill-fitting footwear).
Most surgeons prefer to perform popliteal or tibial arterial bypass because of inferior rates of
limb salvage and patency compared with more proximal procedures. If popliteal or tibial arterial
bypass is unable to restore a palpable foot pulse, pedal bypass has been reported to provide a
more durable and effective limb-salvage procedure for patients with diabetes and ischemic foot
wounds] . Even extensive multisegment occlusive disease in patients with diabetes does not
present an impediment to foot salvage. Whereas serious wound complications may have
disastrous results, they are uncommon after pedal bypass grafting. Adequate control of
preexisting foot infection and careful graft tunneling have been shown to be effective in
avoiding further complications. Angioplasty in the lower extremity is becoming more
progressively utilized. However, it must be emphasized that for angioplasty to be effective, a
distal vessel or feeding vessel must be patent if the more proximal angioplasty is to succeed.
While diabetic ulcers / limb pathologies may be managed in some patients (by Debridement,
antibiotic treatment, use of preparations to stimulate granulation tissue (new collagen and
angiogenesis) and reduction of bacterial burden in the wound), it would be beneficial to have a
pharmaceutical composition that could better treat these conditions and/or alleviate the
symptoms.
For further information, see American Journal of Surgery, Volume 187 • Number 5 Suppl 1 •
May 1,2004, Copyright © 2004 Elsevier.
Coronary Microvascular Dysfunction in diabetes
The correlation between histopathology and microcirculatory dysfunction in diabetes is well
known from old experimental studies and from autopsy, where thickening of the basal
membrane, perivascular fibrosis, vascular rarefication, and capillary hemorrhage are frequently
found. It remains difficult to confirm these data in vivo, although a recent paper demonstrated a
correlation between pathology and ocular micorovascular dysfunction (Am J Physiol 2003;285).
A large amount of clinical studies, however, indicate that not only overt diabetes but also
impaired metabolic control may affect coronary microcirculation (Hypert Res 2002;25:893).
Werner alluded to the important paper by Sambuceti et al (Circulation 2001; 104:1129) showing
the persistence of microvascular dysfunction in patients after successful reopening of the infarct
related artery, and which may explain the increased cardiovascular morbidity and mortality in
these patients. There is mounting evidence from large acute reperfusion studies that morbidity
and mortality are unrelated to the reopening itself of the infarct related artery, but much more
dependent on the T1MI flow+/- myocardial blush (Stone 2002; Feldmann Circulation 2003).
Herrmann indicated, among others, that the integrity of the coronary microcirculation is
probably the most important clincal and prognostic factor in this context (Circulation 2001). The
neutral effect of protection devices (no relevant change for TIMI flow, for ST resolution, or for
MACE) may indicate that a functional impairment of microcirculation is the major determinant
of prognosis. There is also increasing evidence that coronary microvascular dysfunction plays a
major role in non obstructive CAD. Coronary endothelial dysfunction remains a strong
prognostic predictor in these patients.
Diabetic nephropathy (Renal dysfunction in patients with diabetes)
Diabetic nephropathy encompasses microalbuminuria (a microvascular disease effect),
proteinuria and ESRD. Diabetes is the most common cause of kidney failure, accounting for
more than 40 percent of new cases. Even when drugs and diet are able to control diabetes, the
disease can lead to nephropathy and kidney failure. Most people with diabetes do not develop
nephropathy that is severe enough to cause kidney failure. About 16 million people in the
United States have diabetes, and about 100,000 people have kidney failure as a result of
diabetes.
Diabetic retinopathy
In the diabetic state, hyperglycemia leads to decreased retinal blood flow, retinal
hyperpermeability, delays in photoreceptor nerve conduction, and retinal neuronal cell death. In
short duration diabetes, neuronal cell death has been identified within the inner nuclear layer of
the retina. Specifically, apoptosis has been localized to glial cells such as Mueller cells and
astrocytes and has been shown to occur within 1 month of diabetes in the STZ-induced diabetic
rat model. The cause of these events is multi-factorial including activation of the
diacylglycerol/PKC pathway, oxidative stress, and nonenzymatic glycosylation. The
combination of these events renders the retina hypoxic and ultimately leads to the development
of diabetic retinopathy. One possible connection between retinal ischemia and the early changes
in the diabetic retina is the hypoxia-induced production of growth factors such as VEGF. The
master regulator of the hypoxic response has been identified as hypoxia inducible factor-1 (HIF-
1), which controls genes that regulate cellular proliferation and angiogenesis. Prior studies have
demonstrated that inhibition of HIF-1 ubiquitination leads to binding with hypoxia responsive
elements (HRE) and production of VEGF mRNA.
Diabetic Retinopathy is defined as the progressive dysfunction of the retinal vasculature caused
by chronic hyperglycemia. Key features of diabetic retinopathy include microaneurysms, retinal
hemorrhages, retinal lipid exudates, cotton-wool spots, capillary nonperfusion, macular edema
and neovascularization. Associated features include vitreous hemorrhage, retinal detachment,
neovascular glaucoma, premature cataract and cranial nerve palsies.
There are 16 million people in the US with Type 1 and Type 2 diabetes. Within 15 years, 80%
of Type 1 patients have developed diabetic retinopathy while 84% of Type 2 diabetic patients
develop retinopathy within 19 years. These numbers constitute a significant market for
therapeutic agents aimed at ocular diseases of neovasculature. The development of diabetic
retinopathy is time-dependent. Despite optimal blood sugar control, patients with long-standing
disease can be expected to eventually develop some form of retinopathy. The National Society
to Prevent Blindness has estimated that 4 to 6 million diabetics in the U.S. have diabetic
retinopathy. The estimated annual incidence of new cases of proliferative diabetic retinopathy
and diabetic macular edema are 65,000 and 75,000, respectively, with a prevalence of 700,000
and 500,000 respectively. Diabetic retinopathy causes from 12,000 to 24,000 new cases of
blindness in the US every year. Retinopathy is treated by surgical methods, effective in reducing
severe vision loss, but the lasered portions of the retina are irreversibly destroyed. There are no
drug treatments available.
A microvascular disease that primarily affects the capillaries, diabetes mellitus affects the eye
by destroying the vasculature in the conjunctiva, retina and central nervous system. Patients may
present with histories of long-standing injected bulbar conjunctivae along with systemic
complaints of weight loss despite larger than normal appetite (polyphasia), abnormal thirst
(polydypsia) and abnormally frequent urination (polyuria).
19
Fluctuating visual acuity secondary to unstable blood sugar is a common ocular sign. Swelling
within the crystalline lens results in large sudden shifts in refraction as well as premature
cataract formation. Changes in visual acuity will depend upon the severity and stage of the
disease.
In the retina, weakening of the arterioles and capillaries may result in the characteristic
appearance of intraretinal dot and blot hemorrhages, exudates, intraretinal microvascular
abnormalities (IRMA) microaneurysms, edema and cotton wool infarcts. Proliferative diabetic
retinopathy is the result of severe vascular compromise and is visible as neovascularization of
the disc (NVD), neovascularization elsewhere (NVE) and neovascularization of the iris (NVI, or
rubeosis irides). Neurological complications include palsies of the third, fourth and sixth cranial
nerves as well as diabetic papillitis and facial nerve paralysis.
Diabetes mellitus is a genetically influenced group of diseases that share glucose intolerance. It
is characterized as a disorder of metabolic regulation as a result of deficient or malfunctioning
insulin or deficient or malfunctioning cellular insulin receptors.
Biochemistry involving the formation of sorbitol plays a role in the destruction of pericytes,
which are cells that support the vascular endothelium. As the supportive pericytes perish,
capillary endothelium becomes compromised, resulting in the vascular leakage of blood, protein
and lipid. This, in combination with thickened, glucose-laden blood, produces vascular
insufficiency, capillary nonperfusion, retinal hypoxia, altered structure and decreased function.
The formation and release of vasoproliferative factors which play a role in the genesis of retinal
neovascularization are poorly understood.
Most non-vision threatening sequelae of diabetes resolve spontaneously over the course of
weeks to months following medical control. In cases where there are large refractive changes,
patients may require a temporary spectacle prescription until the refraction stabilizes. When
retinopathy threatens the macula or when new blood vessels proliferate, the patient may be
referred for laser photocoagulation. The Diabetic Retinopathy Study (DRS) has conclusively
proven that panretinal photocoagulation was successful in reducing the risk of severe vision loss
in high-risk patients. It defined the high-risk characteristics as: (1) Neovascularization of the
optic disc (NVD) one-quarter to one-third of a disc diameter in size and (2) Neovascularization
elsewhere (NVE) with any vitreous hemorrhage.
Diabetic Macular Edema (DME)
DME is a complication of diabetic retinopathy, a disease affecting the blood vessels of the
retina. Diabetic retinopathy results in multiple abnormalities in the retina, including retinal
thickening and edema, hemorrhages, impeded blood flow, excessive leakage of fluid from blood
vessels and, in the final stages, abnormal blood vessel growth. This blood vessel growth can
lead to large hemorrhages and severe retinal damage. When the blood vessel leakage of diabetic
retinopathy causes swelling in the macula, it is referred to as DME. The principal symptom of
DME is a loss of central vision. Risk factors associated with DME include poorly controlled
blood glucose levels, high blood pressure, abnormal kidney function causing fluid retention,
high cholesterol levels and other general systemic factors.
According to the World Health Organization, diabetic retinopathy is the leading cause of
blindness in working age adults and a leading cause of vision loss in diabetics. The American
Diabetes Association reports that there are approximately 18 million diabetics in the United
States and approximately 1.3 million newly diagnosed cases of diabetes in the United States
each year. Prevent Blindness America and the National Eye Institute estimate that in the United
States there are over 5.3 million people aged 18 or older with diabetic retinopathy, including
approximately 500,000 with DME. The CDC estimates that there are approximately 75,000 new
cases of DME in the United States each year.
Additional Neuropathies
In addition to diabetes, the common causes of neuropathy are herpes zoster infection, chronic or
acute trauma (including surgery) and various neurotoxins. Neuropathic pain is common in
cancer as a direct result of the cancer on peripheral nerves (e.g., compression by a tumor) and as
a side effect of many chemotherapy drugs.
Microvascular disease - Vascular and neural diseases are closely related and intertwined. Blood
vessels depend on normal nerve function, and nerves depends on adequate blood flow. The first
pathological change in the microvasculature is vasoconstriction. As the disease progresses,
neuronal dysfunction correlates closely with the development of vascular abnormalities, such as
capillary basement membrane thickening and endothelial hyperplasia, which contribute to
diminished oxygen tension and hypoxia. Vasodilator agents (e.g., angiotensin-convertingenzyme
inhibitors, a 1-antagonists) can lead to substantial improvements in neuronal blood flow,
with corresponding improvements in nerve conduction velocities.
Clinical manifestations
Neuropathy affects all peripheral nerves: pain fibers, motor neurons, autonomic nerves. It
therefore necessarily can affect all organs and systems since all are innervated. There are several
distinct syndromes based on the organ systems and members affected, but these are by no means
exclusive. A patient can have sensorimotor and autonomic neuropathy or any other combination.
Despite advances in the understanding of the metabolic causes of neuropathy, treatments aimed
at interrupting these pathological processes have been limited by side effects and lack of
efficacy. Thus, treatments are symptomatic and do not address the underlying problems. Agents
for pain caused by sensorimotor neuropathy include tricyclic antidepressants (TCAs), serotonin
reuptake inhibitors (SSRJs) and antiepileptic drugs (AEDs). None of these agents reverse the
pathological processes leading to diabetic neuropathy and none alter the relentless course of the
illness. Thus, it would be useful to have a pharmaceutical composition that could better treat
these conditions and/or alleviate the symptoms.
Additional Retinopathies
Retinal microvasculopathv (AIDS retinopathv)
Retinal microvasculopathy is seen in 100% of AIDS patients. It is characterized by intraretinal
hemorrhages, microaneurysms, Roth spots, cotton-wool spots (microinfarctions of the nerve
fiber layer) and perivascular sheathing . The etiology of the retinopathy is unknown though it
has been thought to be due to circulating immune complexes, local release of cytotoxic
substances, abnormal hemorheology, and HIV infection of endothelial cells. AIDS retinopathy
is now so common that cotton wool spots in a patient without diabetes or hypertension but at
risk for HIV should prompt the physician to consider viral testing. There is no specific treatment
for AIDS retinopathy but its continued presence may prompt a physician to reexamine the
efficacy of the HIV therapy and patient compliance.
Bone marrow transplantation (BMT) retinopathv
Bone marrow transplantation retinopathy was first reported in 1983. It typically occurs within
six months, but it can occur as late as 62 months after BMT. Risk factors such as diabetes and
hypertension may facilitate the development of BMT retinopathy by heightening the ischemic
microvasculopathy. There is no known age, gender or race predilection for development of
BMT retinopathy. Patients present with decreased visual acuity and/or visual field deficit.
Posterior segment findings are typically bilateral and symmetric. Clinical manifestations include
multiple cotton wool spots, telangiectasia, microaneurysms, macular edema, hard exudates and
retinal hemorrhages. Fluorescein angiography demonstrates capillary nonperfusion and dropout,
intraretinal microvascular abnormalities, microaneurysms and macular edema. Although the
precise etiology of BMT retinopathy has not been elucidated, it appears to be affected by several
factors: cyclosporine toxicity, total body irradiation (TBI), and chemotherapeutic agents.
Cyclosporine is a powerful immunomodulatory agent that suppresses graft-versus-host immune
response. It may lead to endothelial cell injury and neurologic side effects, and as a result, it has
been suggested as the cause of BMT retinopathy. However, BMT retinopathy can develop in the
absence of cyclosporine use, and cyclosporine has not been shown to cause BMT retinopathy in
autologous or syngeneic bone marrow recipients. Cyclosporine does not, therefore, appear to be
the sole cause of BMT retinopathy. Total body irradiation (TBI) has also been implicated as the
cause of BMT retinopathy. Radiation injures the retinal microvasculature and leads to ischemic
vasculopathy. Variables such as the total dose of radiation and the time interval between
radiation and bone marrow ablation appear to be important. However, BMT retinopathy can
occur in patients who did not receive TBI, and BMT retinopathy is not observed in solid organ
transplant recipients who received similar doses of radiation. Thus, TBI is not the sole cause, but
it is another contributing factor in development of BMT retinopathy. Chemotherapeutic agents
have been suggested as a potential contributing factor in BMT retinopathy. Medications such as
cisplatin, carmustine, and cyclophosphamide can cause ocular side effects including
papilledema, optic neuritis, visual field deficit and cortical blindness. It has been suggested that
these chemotherapeutic drugs may predispose patients to radiation-induced retinal damages and
enhance the deleterious effect of radiation. In general, patients with BMT retinopathy have a
good prognosis. The retinopathy usually resolves within two to four months after stopping or
lowering the dosage of cyclosporine. In one report, 69 percent of patients experienced complete
resolution of the retinal findings, and 46 percent of patients fully recovered their baseline visual
acuity. Because of the favorable prognosis and relatively non-progressive nature of BMT
retinopathy, aggressive intervention is usually not necessary.
Ischemic conditions
Ischemia can be divided into 2 categories: the first involves the accelerated atherosclerosis that
occurs commonly in patients with diabetes, i.e., in the femoral, popliteal, and posterior tibial
arteries. These vessels, often only 1 or 2 cm in diameter, can develop atherosclerotic plaque,
which seriously decreases blood flow. After large vessels become completely occluded, stroke,
myocardial infarction, ischemia, and nonhealing diabetic foot ulcers can occur. This form of
ischemia is essentially a large-vessel disease.
Post Stroke Dementia
25% of people have dementia after a stroke with many others developing dementia over the
following 5 to 10 years. In addition, many individuals experience more subtle impairments of
their higher brain functions (such as planning skills and speed of processing information) and
are at very high risk of subsequently developing dementia. Very small strokes in the deep parts
of the brain in this process (called microvascular disease) seem to be essential in the process
leading to an identified pattern of brain atrophy specific to post-stroke dementia.
Ocular Ischemic Syndrome
Patients suffering from ocular ischemic syndrome (OIS) are generally elderly, ranging in age
from the 50s to 80s. Males are affected twice as commonly as females. The patient is only rarely
asymptomatic. Decreased vision occurs at presentation in 90 percent of cases, and 40 percent of
patients have attendant eye pain. There may also be an attendant or antecedent history of
transient ischemic attacks or amaurosis fugax. Patients also have significant known or unknown
systemic disease at the time of presentation. The most commonly encountered systemic diseases
are hypertension, diabetes, ischemic heart disease, stroke, and peripheral vascular disease. To a
lesser extent, patients manifest OIS as a result of giant cell arteritis (GCA).
Unilateral findings are present in 80 percent of cases. Common findings may include advanced
unilateral cataract, anterior segment inflammation, asymptomatic anterior chamber reaction,
macular edema, dilated but non-tortuous retinal veins, mid-peripheral dot and blot hemorrhages,
cotton wool spots, exudates, and neovascularization of the disc and retina. There may also be
spontaneous arterial pulsation, elevated intraocular pressure, and neovascularization of the iris
and angle with neovascular glaucoma (NVG). While the patient may exhibit anterior segment
neovascularization, ocular hypotony may occur due to low arterial perfusion to the ciliary body.
Occasionally, there is visible retinal emboli (Hollenhorst plaques).
The findings in OIS are caused by internal carotid artery atheromatous ulceration and stenosis at
the bifurcation of the common carotid artery. Five percent of patients with internal artery
stenosis develop OIS. However, OIS only occurs if the degree of stenosis exceeds 90 percent.
Stenosis of the carotid artery reduces perfusion pressure to the eye, resulting in the abovementioned
ischemic phenomena. Once stenosis reaches 90 percent, the perfusion pressure in the
central retinal artery (CRA) drops only to 50 percent. Often, the reduced arterial pressure
manifests as spontaneous pulsation of the CRA. The findings are variable and may include any
or all of the above findings.
Patients with OIS have significant systemic disease that must be assessed. Cardiac death is the
primary cause of mortality in patients with OIS—the five-year mortality rate is 40 percent. For
this reason, patients with OIS must be referred to a cardiologist for complete serology, EKG,
ECG, and carotid evaluation.
Microvascular Diseases of the Kidney
The kidney is involved in a number of discreet clinicopathologic conditions that affect systemic
and renal microvasculature. Certain of these conditions are characterized by primary injury to
endothelial cells, such as:
• hemolylic-uremic syndrome (HUS) and ihrombotic thrombocytopenic purpura
(TTP) HUS and TTP are closely related diseases characterized by
microangiopathic hemolytic anemia and variable organ impairment Traditionally,
the diagnosis of HUS is made when renal failure is a predominant feature of the
syndrome, as is common in children. In adults, neurologic impairment frequently
predominates and the syndrome is then referred to as TTP. Thrombotic
microangiopathy is the underlying pathologic lesion in both syndromes, and the
clinical and laboratory findings in patients with either HUS or TTP overlap to a
large extent. This has prompted several investigators to regard the two syndromes
as a continuum of a single disease entity. Pathogenesis: Experimental data
strongly suggest that endothelial cell injury is the primary event in the
pathogenesis of HUS/TTP. Endothelial damage triggers a cascade of events that
includes local intravascular coagulation, fibrin deposition, and platelet activation
and aggregation. The end result is the histopathologic finding of thrombotic
microangiopathy common to the different forms of the HUS/TTP syndrome. If
HUS/TTP is left untreated, the mortality rate approaches 90%. Supportive
therapy—including dialysis, antihypertensive medications, blood transfusions,
and management of neurologic complications—contributes to the improved
survival of patients with HUS/TTP. Adequate fluid balance and bowel rest are
important in treating typical HUS associated with diarrhea.
• radiation nephritis - The long-term consequences of renal irradiation in excess
of 2500 rad can be divided into five clinical syndromes:
(i)Acute radiation nephritis occurs in approximately 40% of patients after a latency
period of 6 to 13 months. It is characterized clinically by abrupt onset of hypertension,
proteinuria, edema, and progressive renal failurein most cases leading to end-stage kidneys.
(ii)Chronic radiation nephritis, conversely, has a latency period that varies between 18
months and 14 years after the initial insult. It is insidious in onset and is characterized by
hypertension, proteinuria, and gradual loss of renal function.
(iii)The third syndrome manifests 5 to 19 years after exposure to radiation as benign
proteinuria with normal renal function
(iv)A fourth group of patients exhibits only benign hypertension 2 to 5 years later and
may have variable proteinuria. Late malignant hypertension arises 18 months to 11 years
after irradiation in patients with either chronic radiation nephritis or benign hypertension.
Removal of the affected kidney reversed the hypertension. Radiation-induced damage to the
renal arteries with subsequent renovascular hypertension has been reported.
(v)A syndrome of renal insufficiency analogous to acute radiation nephritis has been
observed in bone marrow transplantation (BMT) patients who were treated with total-body
irradiation (TBI).
It has been reported that irradiation causes endothelial dysfunction but spares vascular smooth
muscle cells in the early postradiation phase. Radiation could directly damage DNA, leading to
decreased regeneration of these cells and denudement of the basement membrane in the
glomerular capillaries and tubules. How this initial insult eventually leads to
glomerulosclerosis, tubule atrophy, and interstitial fibrosis is unclear. It is postulated that
degeneration of the endothelial cell layer may result in intravascular thrombosis in capillaries
and smaller arterioles. This intrarenal angiopathy would then explain the progressive renal
fibrosis and the hypertension that characterize radiation nephritis. A recent study of irradiated
mouse kidneys showed a dose-dependent increase in leukocytes in the renal cortex, suggesting
a role for inflammatory processes in radiation-induced nephritis.
In other kidney diseases, the microvasculature of the kidney is involved in autoimmune
disorders, such as systemic sclerosis (scleroderma). Kidney involvement in systemic sclerosis
manifests as a slowly progressing chronic renal disease or as scleroderma renal crisis (SRC),
which is characterized by malignant hypertension and acute azotemia. It is postulated that SRC
is caused by a Raynaud-like phenomenon in the kidney. Severe vasospasm leads to cortical
ischemia and enhanced production of renin and angiotensin II, which in turn perpetuate renal
vasoconstriction. Hormonal changes (pregnancy), physical and emotional stress, or cold
temperature may trigger the Raynaud-like arterial vasospasm. The role of the renin-angiotensin
system in perpetuating renal ischemia is underscored by the significant benefit of ACE
inhibitors in treating SRC. In patients with SRC who progress to severe renal insufficiency
despite antihypertensive treatment, dialysis becomes a necessity. Both peritoneal dialysis and
hemodialysis have been employed. The End-Stage Renal Disease (ESRD) Network report on
311 patients with systemic sclerosis-induced ESRD dialyzed between 1983 and 1985 revealed
a 33% survival rate at 3 years.
The renal microcirculation can also be affected in sickle cell disease, to which the kidney is
particularly susceptible because of the low oxygen tension attained in the deep vessels of the
renal medulla as a result of countercurrent transfer of oxygen along the vasa recta. The smaller
renal arteries and arterioles can also be the site of thromboembolic injury from cholesterolcontaining
material dislodged from the walls of the large vessels.
Taken as a group, diseases that cause transient or permanent occlusion of renal
microvasculature uniformly result in disruption of glomerular perfusion, and hence of the
glomerular filtration rate, thereby constituting a serious threat to systemic homeostasis.
Acute Renal Failure (ARF)
ARF can be caused by microvascular or macrovascular disease (major renal artery occlusion or
severe abdominal aortic disease). The classic microvascular diseases often present with
microangiopathic hemolysis and acute renal failure occurring because of glomerular capillary
thrombosis or occlusion, often with accompanying thrombocytopenia. Typical examples of
these diseases include:
a) Thrombotic thrombocytopenic purpura - The classic pentad in thrombotic
thrombocytopenic purpura includes fever, neurologic changes, renal failure,
microangiopathic hemolytic anemia and thrombocytopenia.
b) Hemolvtic uremic syndrome - Hemolytic uremic syndrome is similar to thrombotic
thrombocytopenic purpura but does not present with neurologic changes.
c) HELLP syndrome (hemolvsis. elevated liver enzymes and low platelets). HELLP
syndrome is a type of hemolytic uremic syndrome that occurs in pregnant women with
the addition of transaminase elevations.
Acute renal failure can present in all medical settings but is predominantly acquired in hospitals.
The condition develops in 5 percent of hospitalized patients, and approximately 0.5 percent of
hospitalized patients require dialysis. Over the past 40 years, the survival rate for acute renal
failure has not improved, primarily because affected patients are now older and have more
comorbid conditions. Infection accounts for 75 percent of deaths in patients with acute renal
failure, and cardio-respiratory complications are the second most common cause of death.
Depending on the severity of renal failure, the mortality rate can range from 7 percent to as high
as 80 percent. Acute renal failure can be divided into three categories: Prerenal, intrinsic and
postrenal ARF. Intrinsic ARF is subdivided into four categories: tubular disease, glomerular
disease, vascular disease (includes microvascular) and interstitial disease.
Progressive Renal Disease
There is evidence that progressive renal disease is characterized by a progressive loss of the
microvasculature. The loss of the microvasculature correlates directly with the development of
glomerular and tubulointerstitial scarring. The mechanism is mediated in part by a reduction in
the endothelial proliferative response, and this impairment in capillary repair is mediated by
alteration in the local expression of both angiogenic (vascular endothelial growth factor) and
antiangiogenic (thrombospondin 1) factors in the kidney. The alteration in balance of angiogenic
growth factors is mediated by both macrophage-associated cytokines (interleukin-lfi) and
vasoactive mediators. Finally, there is intriguing evidence that stimulation of angiogenesis
and/or capillary repair may stabilize renal function and slow progression and that this benefit
occurs independently of effects on BP or proteinuria.
For further information see Brenner & Rector's The Kidney, 7th ed., Copyright © 2004 Elsevier:
Chapter 33 - Microvascular diseases of the kidney and also Tiwari andVikrant Journal of Indian
Academy of Clinical Medicine Vol.5, No.l Review Article- Sepsis and the Kidney.
In conclusion, current modes of therapy for the prevention and/or treatment of COPD, macular
degeneration and microvascular diseases are unsatisfactory and there is a need therefore to
develop novel compounds for this purpose. All the diseases and indications disclosed herein
above, as well as other diseases and conditions described herein such as MI may also be treated
by the novel compounds of this invention.
RTP801
Gene RTP801, was first reported by the assignee of the instant application. US Patent Nos.
6455674, 6555667, and 6740738, all assigned to the assignee of the instant application, disclose
and claim per se the RTP801 polynucleotide and polypeptide, and antibodies directed toward
the polypeptide. RTP801 represents a unique gene target for hypoxia-inducible factor-1 (HIF-1)
that may regulate hypoxia-induced pathogenesis independent of growth factors such as VEGF.
The inventor of the instant invention has made discoveries leading to the novel concept of
inhibiting gene RTP801 with the purpose of improving various respiratory disorders.
The following patent applications and publications give aspects of background information.
WO 2001070979 relates to nucleic acid markers which are overexpressed in ovarian cancer
cells.
US 6673549 discloses a combination comprising cDNAs that are differentially expressed in
response to steroid treatment.
US application 2003165864 relates to cDNAs that are differentially expressed in cells treated
with a DNA demethylating agent.
US application 2003108871 relates to a composition comprising several cDNAs that are
differentially expressed in treated human C3A liver cell cultures, allegedly useful for treating
liver disorders.
US application 2002119463 discloses a new composition, useful for treating and diagnosing
prostate cancer, said composition comprising human cDNAs that are differentially expressed in
prostate cancer.
WO 2004018999 discloses a method for assessing, characterizing, monitoring, preventing and
treating cervical cancer.
EP 1394274 relates to a method of testing for bronchial asthma or chronic obstructive
pulmonary disease by comparing the expression level of a marker gene in a biological sample
from a subject with the expression level of the gene in a sample from a healthy subject.
WO 2002101075 relates to an isolated nucleic acid molecule useful for detecting,
characterizing, preventing and treating human cervical cancers.
WO 2003010205 relates to inhibiting angiogenesis for treating wound healing, retinopathy,
ischemia, inflammation, microvasculopathy, bone healing and skin inflammation .
WO 2002046465 relates to identifying a gene involved in disease for treating hypoxia- regulated
conditions.
WO 2002031111 relates to allegedly novel polypeptides and their encoded proteins, and many
uses therefore are provided.
WO 2001012659 relates to nucleic acids useful in recombinant DNA methodologies.
WO 2001077289 discloses six hundred and twenty three polynucleotides derived from a variety
of human tissue sources.
WO 2003101283 relates to a combination which comprises many cDNAs and proteins allegedly
differentially expressed in respiratory disorders.
JP 2003259877 relates to many hepatic fibrosis disease markers.
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RTP801, Involved in Apoptosis. MOLECULAR AND CELLULAR BIOLOGY, Apr. 2002, p.
2283-2293;this paper, co-authored by the inventor of the present invention, details the discovery
of the RTP801 gene (a then novel H1F-1-dependent gene
Anat Brafrnan, et al. Inhibition of Oxygen-Induced Retinopathy in RTP801-Deficient Mice.
Invest Ophthalmol Vis Sci. 2004 Oct; 45 (10): 3796-805; also co-authored by the inventor of the
present invention, this paper demonstrates that in RTP801 knock out mice, hyperoxia does not
cause degeneration of the retinal capillary network.
Leif W. Ellisen, et al. REDDl, a Developmentally Regulated Transcriptional Target ofp63 and
p53, Links p63 to Regulation of Reactive Oxygen Species. Molecular Cell, Vol. 10, 995-1005,
November, 2002;this paper demonstrates that overexpression of RTP801 (referred to therein as
REDDl) leads to increased production of reactive oxygen species.
Richard DR, Berra E, and Pouyssegur J. Non-hypoxic pathway mediates the induction of
hypoxia-inducible factor 1 alpha in vascular smooth muscle cells. J Biol. Chem. 2000, Sepl;
275(35): 26765-71 this paper demonstrates that HIF-1-dependent transcription may be induced
by excessive production of reactive oxygen species.
Rangasami T, et al., Genetic ablation ofNrft enhances susceptibility to cigarette smoke-induced
emphysema in mice. Submitted to Journal of Clinical Investigation. This work relates to mice
with a compromised antoxidant defence (due to a germline inactivation of RTP801, therein
termed Nrf2).
SUMMARY OF THE INVENTION
The present invention provides novel methods and compositions for treating microvascular
disorders, macular degeneration, respiratory disorders, and spinal cord injury or disease.
In one embodiment, novel molecules which inhibit RTP801 and can be used to treat various
diseases and indications are provided.
In another embodiment, the present invention provides a method of treating a patient suffering
from a microvascular disorder, macular degeneration or a respiratory disorder, comprising
administering to the patient a pharmaceutical composition comprising an RTP801 inhibitor.
Another embodiment of the present invention concerns a method for treating a patient suffering
from COPD, comprising administering to the patient a pharmaceutical composition comprising
a therapeutically effective amount of an RTP801 inhibitor. In one embodiment the inhibitor is
an siRNA molecule, an antisense molecule, an antibody (such as a neutralizing antibody), a
dominant negative peptide or a ribozyme.
Another embodiment of the present invention concerns a method for treating a patient suffering
from macular degeneration, comprising administering to the patient a pharmaceutical
composition comprising a therapeutically effective amount of an RTP801 inhibitor. In one
embodiment the inhibitor is an siRNA molecule, an antisense molecule, an antibody (such as a
neutralizing antibody), a dominant negative peptide or a ribozyme.
Another embodiment of the present invention concerns a method for treating a patient suffering
from a microvascular disorder, comprising administering to the patient a pharmaceutical
composition comprising a therapeuticaliy effective amount of an RTP801 inhibitor. In one
embodiment the inhibitor is an siRNA molecule, an antisense molecule, an antibody (such as a
neutralizing antibody), a dominant negative peptide or a ribozyme.
An additional embodiment of the present invention provides for the use of a therapeuticaliy
effective amount of an RTP801 inhibitor for the preparation of a medicament for promoting
recovery in a patient suffering from a respiratory disorder. In one embodiment the respiratory
disorder is COPD and the inhibitor is preferably an siRNA.
An additional embodiment of the present invention provides for the use of a therapeuticaliy
effective dose of an RTP801 inhibitor for the preparation of a medicament for promoting
recovery in a patient suffering from macular degeneration. In one embodiment the macular
degeneration is AMD and the inhibitor is preferably an siRNA.
An additional embodiment of the present invention provides for the use of a therapeuticaliy
effective amount of an RTP801 inhibitor for the preparation of a medicament for promoting
recovery in a patient suffering from a microvascular disorder. In one embodiment the
microvascular disorder is diabetic retinopathy and the inhibitor is preferably an siRNA.
DETAILED DESCRIPTION OF THE INVENTION
The present invention, in some of its embodiments, concerns inhibition of the RTP801 gene or
polypeptide for the treatment of eye diseases, respiratory disorders and microvascular disorders,
inter alia. As will be described herein, the preferred inhibitors to be used with the present invention
are biological molecules.
Without being bound by theory, the inventors of the present invention have found that RTP801
is involved in various disease states including microvascular disorders, eye diseases, respiratory
disorders , and spinal cord injury and disease, and it would be beneficial to inhibit RTP801 in
order to treat any of said diseases or disorders. Methods, molecules and compositions which
inhibit RTP801 are discussed herein at length, and any of said molecules and/or compositions
may be beneficially employed in the treatment of a patient suffering from any of said conditions.
The present invention provides methods and compositions for inhibiting expression of the
RTP801 gene in vivo. In general, the method includes administering oligoribonucleotides,
such as small interfering RNAs (i. e., siRNAs) that are targeted to a particular mRNA and
hybridise to it, or nucleic acid material that can produce siRNAs in a cell, in an amount
sufficient to down-regulate expression of a target gene by an RNA interference mechanism.
In particular, the subject method can be used to inhibit expression of the RTP801 gene for
treatment of respiratory disorders, microvascular disorders or eye disorders.
Thus, in one embodiment the present invention provides for a method of treating a patient
suffering from a microvascular disorder, aeye disease or a respiratory disorder, comprising
administering to the patient a pharmaceutical composition comprising an RTP801 inhibitor in a
therapeutically effective amount so as to thereby treat the patient. The invention further provides
a method of treating a patient suffering from a microvascular disorder, aeye disease or
respiratory disorder, comprising administering to the patient a pharmaceutical composition
comprising an RTP801 inhibitor, in a dosage and over a period of time sufficient to promote
recovery. The eye disease may be macular degeneration such as age-related macular
degeneration (AMD), inter alia. The microvascular disorder may be diabetic retinopathy or
acute renal failure, inter alia. The respiratory disorder may be chronic obstructive pulmonary
disease (COPD), emphysema, chronic bronchitis, asthma and lung cancer, inter alia. The
RTP801 inhibitor may be selected from a large variety of molecules, including but not limited to
compounds such as polynucleotides, AS fragments, RNA molecules which target the RTP801
gene mRNA such as ribozymes or siRNAs (such as the siRNAs of Tables A-C and in particular,
siRNA Nos:14, 22, 23, 25, 27, 39, 41, 42, 49 and 50 of Table A), or expression vectors
comprising them; polypeptides such as dominant negatives, antibodies (such as an antibody
which specifically binds to an epitope present within a polypeptide which comprises consecutive
amino acids, the sequence of which is set forth in Figure 2 (SEQ ID No:2)), or, in some cases,
enzymes. Additionally, the RTP801 inhibitor may be a chemical inhibitor such as a small
molecule, e.g., chemical molecules with a low molecular weight e.g. a molecular weight below
2000 daitons. Specific RTP801 inhibitors are given below.
The present invention further provides a method for treating a patient suffering from macular
degeneration, COPD or diabetic retinopathy, comprising administering to the patient a
pharmaceutical composition comprising a therapeutically effective dose of an RTP801 inhibitor
comprising a polynucleotide which specifically hybridizes to mRNA transcribed from the
RTP801 gene and / or down regulates the expression of the RTP801 gene so as to thereby treat
the patient. The polynucleotide may be an siRNA comprising consecutive nucleotides having a
sequence identical to any one of the sequences set forth in Tables A-C (SEQ ID NOs:3-344) and
in particular, siRNA Nos: 14,22,23,25, 27, 39, 41,42,49 and 50 of Table A.
Further, an additional embodiment of the present invention concerns a method for treating a
patient suffering from a microvascular disorder, a respiratory disorder or an eye disease,
comprising administering to the patient a pharmaceutical composition comprising a
therapeutically effective dose of an RTP801 inhibitor comprising an siRNA molecule,
optionally an siRNA molecule detailed in any one of Tables A-C, in a dosage and over a period
of time so as to thereby treat the patient.
An additional method for treating a patient suffering from a microvascular disorder, a
respiratory disorder or an eye disease is provided, comprising administering to the patient
pharmaceutical composition comprising a therapeutically effective dose of an RNA molecule
which targets the RTP801 gene mRNA in a dosage and over a period of time so as to thereby
treat the patient. The RNA molecule may be an si RNA molecule, such as an siRNA molecule
detailed in Tables A-C and in particular, siRNA Nos:14, 22, 23, 25, 27, 39, 41, 42, 49 and 50 of
Table A, or a ribozyme.
The present invention further provides a method for treating a patient suffering from a
respiratory disorder, a microvascular disorder or an eye disease or any of the conditions
disclosed herein, comprising administering to the patient a pharmaceutical composition
comprising a therapeutically effective dose of an siRNA molecule which targets the RTP801
gene mRNA, optionally an siRNA molecule detailed in Tables A-C, in a dosage and over a
period of time so as to thereby treat the patient. Further, the eye disease may be macular
degeneration such as age-related macular degeneration (AMD); the microvascular disorder may
be diabetic retinopathy or acute renal failure; the respiratory disorder may be COPD and the
aspects of COPD being treated may comprise, but are not limited to, emphysema, chronic
bronchitis, or both.
"Treating a disease" refers to administering a therapeutic substance effective to ameliorate
symptoms associated with a disease, to lessen the severity or cure the disease, or to prevent the
disease from occurring.
A "therapeutically effective dose" refers to an amount of a pharmaceutical compound or
composition which is effective to achieve an improvement in a patient or his physiological systems
including, but not limited to, improved survival rate, more rapid recovery, or improvement or
elimination of symptoms, and other indicators as are selected as appropriate determining measures
by those skilled in the art.
The methods of treating the diseases disclosed herein and included in the present invention may
include administering an RTP801 inhibitor in conjunction with an additional RTP801 inhibitor,
a substance which improves the pharmacological properties of the active ingredient as detailed
below, or an additional compound known to be effective in the treatment of the disease to be
treated, such as macular degeneration, COPD, ARF, DR, inter alia. By "in conjunction with" is
meant prior to, simultaneously or subsequent to. Further detail on exemplary conjoined therapies
is given below.
In another embodiment, the present invention provides for the use of a therapeutically effective
dose of an RTP801 inhibitor for the preparation of a medicament for promoting recovery in a
patient suffering from macular degeneration, COPD, ARF, DR, or any other eye disease,
microvascular or respiratory condition as detailed above, and the use of a therapeutically
effective dose of an RTP801 inhibitor for the preparation of a medicament for treating said
diseases and conditions. In this embodiment, the RTP801 inhibitor may comprise a
polynucleotide which comprises consecutive nucleotides having a sequence which comprises an
antisense sequence to the sequence set forth in Figure 1 (SEQ ID No: 1). Additionally, the
RTP801 inhibitor may be an expression vector comprising a polynucleotide having a sequence
which is an antisense sequence to the sequence set forth in Figure 1 (SEQ ID No:l). The
RTP801 inhibitor according to said uses may also be an antibody, such as a neutralizing
antibody which specifically binds to an epitope present within a polypeptide which comprises
consecutive amino acids, the sequence of which is set forth in Figure 2 (SEQ ID No:2).
Additionally, the RTP801 inhibitor may be an RNA molecule which targets the RTP801 gene
mRNA optionally an siRNA, optionally an siRNA comprising consecutive nucleotides having a
sequence identical to any one of the sequences set forth in Tables A-C (SEQ ID NOs:3-344) and
in particular, siRNA Nos: 14, 22, 23,25,27, 39,41,42,49 and 50 of Table A, or a ribozyme.
Thus, according to the information disclosed herein, the RTP801 inhibitor to be used with any
of the methods disclosed herein, in any of the uses disclosed herein and in any of the
pharmaceutical compositions disclosed herein, may be selected from the group consisting of an
siRNA molecule, a vector comprising an siRNA molecule, a vector which can express an
siRNA molecule and any molecule which is endogenously processed into an siRNA molecule.
As detailed herein, said siRNA molecule is preferably an siRNA comprising consecutive
nucleotides having a sequence identical to any one of the sequences set forth in Tables A-C
(SEQ ID NOs:3-344) and in particular, siRNA Nos: 14, 22, 23, 25, 27, 39, 41, 42, 49 and 50 of
Table A.
"Respiratory disorder" refers to conditions, diseases or syndromes of the respiratory system
including but not limited to pulmonary disorders of all types including chronic obstructive
pulmonary disease (COPD), emphysema, chronic bronchitis, asthma and lung cancer, infer alia.
Emphysema and chronic bronchitis may occur as part of COPD or independently.
"Microvascular disorder" refers to any condition that affects microscopic capillaries and
lymphatics, in particular vasospastic diseases, vasculitic diseases and lymphatic occlusive
diseases. Examples of microvascular disorders include, inter alia: eye disorders such as
Amaurosis Fugax (embolic or secondary to SLE), apla syndrome, Prot CS and ATII1 deficiency,
microvascular pathologies caused by IV drug use, dysproteinemia, temporal arteritis, anterior
ischemic optic neuropathy, optic neuritis (primary or secondary to autoimmune diseases),
glaucoma, von hippel lindau syndrome, corneal disease, corneal transplant rejection cataracts,
Bales' disease, frosted branch angiitis, encircling buckling operation, uveitis including pars
planitis, choroidal melanoma, choroidal hemangioma, optic nerve aplasia; retinal conditions
such as retinal artery occlusion, retinal vein occlusion, retinopathy of prematurity, HIV
retinopathy, Purtscher retinopathy, retinopathy of systemic vasculitis and autoimmune diseases,
diabetic retinopathy, hypertensive retinopathy, radiation retinopathy, branch retinal artery or
vein occlusion, idiopathic retinal vasculitis, aneurysms, neuroretinitis, retinal embolization,
acute retinal necrosis, Birdshot retinochoroidopathy, long-standing retinal detachment; systemic
conditions such as Diabetes mellitus, diabetic retinopathy (DR), diabetes-related microvascular
pathologies (as detailed herein), hyperviscosity syndromes, aortic arch syndromes and ocular
ischemic syndromes, carotid-cavernous fistula, multiple sclerosis, systemic lupus
erythematosus, arteriolitis with SS-A autoantibody, acute multifocal hemorrhagic vasculitis,
vasculitis resulting from infection, vasculitis resulting from Beliefs disease, sarcoidosis,
coagulopathies, neuropathies, nephropathies, microvascular diseases of the kidney, and ischemic
microvascular conditions, inter alia
Microvascular disorders may comprise a neovascular element.The term "neovascular disorder"
refers to those conditions where the formation of blood vessels (neovascularization) is harmful to
the patient. Examples of ocular neovascularization include: retinal diseases (diabetic retinopathy,
diabetic Macular- Edema, chronic glaucoma, retinal detachment, and sickle cell retinopathy);
rubeosis iritis; proliferative vitreo-retinopathy; inflammatory diseases; chronic uveitis; neoplasms
(retinoblastoma, pseudoglioma and melanoma); Fuchs' heterochromic iridocyclitis; neovascuJar
glaucoma; corneal neovascularization (inflammatory, transplantation and developmental
hypoplasia of the iris); neovascularization following a combined vitrectomy and lensectomy;
vascular diseases (retinal ischemia, choroidal vascular insufficiency, choroidal thrombosis and
carotid artery ischemia); neovascularization of the optic nerve; and neovascularization due to
penetration of the eye or contusive ocular injury. All these neovascular conditions may be treated
using the compounds and pharmaceutical compositions of the present invention.
"Eye disease" refers to refers to conditions, diseases or syndromes of the eye including but not
limited to any conditions involving choroidal neovascularization (CNV), wet and dry AMD,
ocular histoplasmosis syndrome, angiod streaks, ruptures in Bruch's membrane, myopic
degeneration, ocular tumors, retinal degenerative diseases and retinal vein occlusion
(RVO). Some conditions disclosed herein, such as DR, which may be treated according to
the methods of the present invention have been regarded as either a microvascular disorder
and an eye disease, or both, under the definitions presented herein.
"RTP801 gene" refers to the RTP801 coding sequence open reading frame, as shown in Figure 1
(SEQ ID NO:1), or any homologous sequence thereof preferably having at least 70% identity,
more preferable 80% identity, even more preferably 90% or 95% identity. This encompasses
any sequences derived from SEQ ID NO:1 which have undergone mutations, alterations or
modifications as described herein. Thus, in a preferred embodiment RTP801 is encoded by a
nucleic acid sequence according to SEQ. ID. NO. 1. It is also within the present invention that
the nucleic acids according to the present invention are only complementary and identical,
respectively, to a part of the nucleic acid coding for RTP801 as, preferably, the first stretch and
first strand is typically shorter than the nucleic acid according to the present invention. It is also
to be acknowledged that based on the amino acid sequence of RTP801 any nucleic acid
sequence coding for such amino acid sequence can be perceived by the one skilled in the art
based on the genetic code. However, due to the assumed mode of action of the nucleic acids
according to the present invention, it is most preferred that the nucleic acid coding for RTP801,
preferably the mRNA thereof, is the one present in the organism, tissue and/or cell, respectively,
where the expression of RTP801 is to be reduced.
"RTP801 polypeptide" refers to the polypeptide of the RTP801 gene, and is understood to
include, for the purposes of the instant invention, the terms "RTP779", "REDD1", "Ddit4",
"FLJ20500", "Dig2", and "PRF1", derived from any organism, optionally man, splice variants
and fragments thereof retaining biological activity, and homologs thereof, preferably having at
least 70%, more preferably at least 80%, even more preferably at least 90% or 95% homology
thereto. In addition, this term is understood to encompass polypeptides resulting from minor
alterations in the RTP801 coding sequence, such as, inter alia, point mutations, substitutions,
deletions and insertions which may cause a difference in a few amino acids between the
resultant polypeptide and the naturally occurring RTP801. Polypeptides encoded by nucleic acid
sequences which bind to the RTP801 coding sequence or genomic sequence under conditions of
highly stringent hybridization, which are well-known in the art (for example Ausubel et al.,
Current Protocols in Molecular Biology, John Wiley and Sons, Baltimore, Maryland (1988),
updated in 1995 and 1998), are also encompassed by this term. Chemically modified RTP801 or
chemically modified fragments of RTP801 are also included in the term, so long as the
biological activity is retained. RTP801 preferably has or comprises an amino acid sequence
according to SEQ. ID. NO. 2. It is acknowledged that there might be differences in the amino
acid sequence among various tissues of an organism and among different organisms of one
species or among different species to which the nucleic acid according to the present invention
can be applied in various embodiments of the present invention. However, based on the
technical teaching provided herein, the respective sequence can be taken into consideration
accordingly when designing any of the nucleic acids according to the present invention-
Particular fragments of RTP801 include amino acids 1-50, 51-100,103-150, 151-200 and 201-
232 of the sequence shown in Figure 2. Further particular fragments of RTP801 include amino
acids 25-74, 75-124, 125-174,175-224 and 225-232 of the sequence shown in Figure 2.
RTP801 as used herein is a protein described, among others, in WO 99/09046. RTP801 which is
also referred to as RTP801, has been described as a transcriptional target of HIF-la by Shoshani T
et al. (Shoshani et al., 2002, Mol Cell Biol, 22, 2283-93). Furthermore the study by Ellisen et al.
(Ellisen et al., Mol Cell, 10, 995-1005) has identified RTP801 as a p53-dependent DNA damage
response gene and as a p63-dependent gene involved in epithelial differentiation. Also, RTP801
mirrors the tissue-specific pattern of the p53 family member p63, is effective similar to or in
addition to TP 63, is an inhibitor to in vitro differentiation , and is involved in the regulation of
reactive oxygen species. Apart from that, RTP801 is responsive to hypoxia-responsive transcription
factor hypoxia-inducible factor 1 (HIF-1) and is typically up-regulated during hypoxia both in vitro
and in vivo in an animal model of ischemic stroke. RTP801 appears to function in the regulation of
reactive oxygen species (ROS) and ROS levels and reduced sensitivity to oxidative stress are both
increased following ectopic expression RTP801 (Ellisen et al. 2002, supra; Soshani et al. 2002,
supra). Preferably, RTP801 is a biologically active RTP801 protein which preferably exhibits at
least one of those characteristics, preferable two or more and most preferably each and any
of these characteristics.
A related gene to RTP801 is RT801L, also referred to as "REDD2", was discovered by the
inventors of the present invention. RTP801L is homologous to RTP801, and reacts in a similar
manner to oxidative stress; thus, RTP801L probably possesses some similar functions with
RTP801.
Without being bound by theory, RTP801 being a stress-inducible protein (responding to
hypoxia, oxidative stress, termal stress, ER stress) is a factor acting in fine-tuning of cell
response to energy disbalance. As such, it is a target suitable for treatment of any disease where
cells should be rescued from apoptosis due to stressful conditions (e.g. diseases accompanied by
death of normal cells) or where cells, which are adapted to stressful conditions due to changes in
RTP801 expression (e.g. cancer cells), should be killed. In the latter case, RTP801 may be
viewed as a survival factor for cancer cells and its inhibitors may treat cancer as a monotherapy
or as sensitising drugs in compbination with chemotherapy or radiotherapy.
The term "polynucleotide" refers to any molecule composed of DNA nucleotides, RNA
nucleotides or a combination of both types, i.e. that comprises two or more of the bases
guanidine, cytosine, thymidine, adenine, uracil or inosine, inter alia. A polynucleotide may
include natural nucleotides, chemically modified nucleotides and synthetic nucleotides, or
chemical analogs thereof. The term includes "oligonucleotides" and encompasses "nucleic
acids".
The term "amino acid" refers to a molecule which consists of any one of the 20 naturally occurring
amino acids, amino acids which have been chemically modified (see below), or synthetic amino
acids.
The term "polypeptide" refers to a molecule composed of two or more amino acids residues.
The term includes peptides, polypeptides, proteins and peptidomimetics.
A "peptidomimetic" is a compound containing non-peptidic structural elements that is capable of
mimicking the biological action(s) of a natural parent peptide. Some of the classical peptide
characteristics such as enzymatically scissille peptidic bonds are normally not present in a
peptidomimetic.
By the term "dominant negative peptide" is meant a polypeptide encoded by a cDNA fragment
that encodes for a part of a protein (see Herskowitz I.: Functional inactivation of genes by
dominant negative mutations. Nature. 1987 Sep 17-23;329(6136):219-22. Review; Roninson IB
et al., Genetic suppressor elements: new tools for molecular oncology—thirteenth Cornelius P.
Rhoads Memorial Award Lecture. Cancer Res. 1995 Sep 15;55(18):4023). This peptide can
have a different function from the protein from which it was derived. It can interact with the full
protein and inhibit its activity or it can interact with other proteins and inhibit their activity in
response to the full-length (parent) protein. Dominant negative means that the peptide is able to
overcome the natural parent protein and inhibit its activity to give the cell a different
characteristic, such as resistance or sensitization to death or any cellular phenotype of interest.
For therapeutic intervention the peptide itself may be delivered as the active ingredient of a
pharmaceutical composition, or the cDNA can be delivered to the cell utilizing known methods.
Preparation of peptides and polvpeptides
Polypeptides may be produced via several methods, for example:
43
1) Synthetically:
Synthetic polypeptides can be made using a commercially available machine, using the known
sequence of RTP801 or a portion thereof.
2) Recombinant Methods:
A preferred method of making the RTP801 polypeptides of fragments thereof is to clone a
polynucleotide comprising the cDNA of the RTP801 gene into an expression vector and culture
the cell harboring the vector so as to express the encoded polypeptide, and then purify the
resulting polypeptide, all performed using methods known in the art as described in, for example,
Marshak et al., "Strategies for Protein Purification and Characterization. A laboratory course
manual" CSHL Press (1996). (in addition, see Bibl Haematol. 1965;23:1165-74 Appl Microbiol.
1967 Jul; 15(4):851-6; Can J Biochem. 1968 May;46(5):441-4; Biochemistry. 1968
Jul;7(7):2574-80; Arch Biochem Biophys. 1968 Sep 10;126(3):746-72; Biochem Biophys Res
Commun. 1970 Feb 20;38(4):825-30).).
The expression vector can include a promoter for controlling transcription of the heterologous
material and can be either a constitutive or inducible promoter to allow selective transcription.
Enhancers that can be required to obtain necessary transcription levels can optionally be
included. The expression vehicle can also include a selection gene.
Vectors can be introduced into cells or tissues by any one of a variety of methods known within
the art. Such methods can be found generally described in Sambrook et al., Molecular Cloning:
A Laboratory Manual, Cold Springs Harbor Laboratory, New York (1989, 1992), in Ausubel et
al., Current Protocols in Molecular Biology, John Wiley and Sons, Baltimore, Maryland (1989),
Vega et al., Gene Targeting, CRC Press, Ann Arbor, MI (1995), Vectors: A Survey of Molecular
Cloning Vectors and Their Uses, Butterworths, Boston MA (1988) and Gilboa et al. (1986).
3) Purification from natural sources:
RTP801 polypeptide, or naturally occurring fragments thereof, can be purified from natural
sources (such as tissues) using many methods known to one of ordinary skill in the art, such as
for example: immuno-precipitation with anti- RTP801 antibody, or matrix-bound affinity
chromatography with any molecule known to bind RTP801.
Protein purification is practiced as is known in the art as described in, for example, Marshak et
al., "Strategies for Protein Purification and Characterization. A laboratory course manual."
CSHL Press (1996).
By "biological effect of RTP801" or "RTP801 biological activity" is meant the effect of
RTP801 in respiratory disorders, which may be direct or indirect, and includes, without being
bound by theory, the effect of RTP801 on apoptosis of alveolar cells induced by hypoxic or
hyperoxic conditions. The indirect effect includes, but is not limited to, RTP801 binding to or
having an effect on one of several molecules, which are involved in a signal transduction
cascade resulting in apoptosis.
"Apoptosis" refers to a physiological type of cell death which results from activation of some
cellular mechanisms, i.e. death that is controlled by the machinery of the cell. Apoptosis may, for
example, be the result of activation of the cell machinery by an external trigger, e.g. a cytokine or
anti-FAS antibody, which leads to cell death or by an internal signal. The term "programmed cell
death" may also be used interchangeably with "apoptosis".
"Apoptosis-related disease" refers to a disease whose etiology is related either wholly or
partially to the process of apoptosis. The disease may be caused either by a malfunction of the
apoptotic process (such as in cancer or an autoimmune disease) or by overactivity of the
apoptotic process (such as in certain neurodegenerative diseases). Many diseases in which
RTP801 is involved are apoptosis-related diseases. For example, apoptosis is a significant
mechanism in dry AMD, whereby slow atrophy of photoreceptor and pigment epithelium cells,
primarily in the central (macular) region of retina takes place. Neuroretinal apoptosis is also a
significant mechanism in diabetic retinopathy.
An "inhibitor" is a compound which is capable of inhibiting the activity of a gene or the product of
such gene to an extent sufficient to achieve a desired biological or physiological effect. An
"RTP801 inhibitor" is a compound which is capable of inhibiting the activity of the RTP801 gene
or RTP801 gene product, particularly the human RTP801 gene or gene product. Such inhibitors
include substances that affect the transcription or translation of the gene as well as substances that
affect the activity of the gene product. An RTP801 inhibitor may also be an inhibitor of the
RTP801 promoter. Examples of such inhibitors may include, inter alia: polynucleotides such as AS
fragments, siRNA, or vectors comprising them; polypeptides such as dominant negatives,
antibodies, and enzymes; catalytic RNAs such as ribozymes; and chemical molecules with a low
molecular weight e.g. a molecular weight below 2000 daltons. Specific RTP801 inhibitors are
given below.
"Expression vector" refers to a vector that has the ability to incorporate and express heterologous
DNA fragments in a foreign cell. Many prokaryotic and eukaryotic expression vectors are known
and/or commercially available. Selection of appropriate expression vectors is within the knowledge
of those having skill in the art.
The term "antibody" refers to IgG, IgM, IgD, IgA, and IgE antibody, inter alia. The definition
includes polyclonal antibodies or monoclonal antibodies. This term refers to whole antibodies or
fragments of antibodies comprising an antigen-binding domain, e.g. antibodies without the Fc
portion, single chain antibodies, miniantibodies, fragments consisting of essentially only the
variable, antigen-binding domain of the antibody, etc. The term "antibody" may also refer to
antibodies against polynucleotide sequences obtained by cDNA vaccination. The term also
encompasses antibody fragments which retain the ability to selectively bind with their antigen or
receptor and are exemplified as follows, inter alia:
(1) Fab, the fragment which contains a monovalent antigen-binding fragment of an
antibody molecule which can be produced by digestion of whole antibody with the
enzyme papain to yield a light chain and a portion of the heavy chain;
(2) (Fab')2, the fragment of the antibody that can be obtained by treating whole antibody
with the enzyme pepsin without subsequent reduction; F(ab'2) is a dimer of two Fab
fragments held together by two disulfide bonds;
(3) Fv, defined as a genetically engineered fragment containing the variable region of the
light chain and the variable region of the heavy chain expressed as two chains; and
(4) Single chain antibody (SCA), defined as a genetically engineered molecule
containing the variable region of the light chain and the variable region of the heavy
chain linked by a suitable polypeptide linker as a genetically fused single chain
molecule.
By the term "epitope" as used in this invention is meant an antigenic determinant on an antigen
to which the antibody binds. Epitopic determinants usually consist of chemically active surface
groupings of molecules such as amino acids or sugar side chains and usually have specific threedimensional
structural characteristics, as well as specific charge characteristics.
Preparation of anti- RTP8Q1 antibodies
Antibodies which bind to RTP801 or a fragment derived therefrom may be prepared using an
intact polypeptide or fragments containing smaller polypeptides as the immunizing antigen. For
example, it may be desirable to produce antibodies that specifically bind to the N- or C- terminal
or any other suitable domains of the RTP801. The polypeptide used to immunize an animal can
be derived from translated cDNA or chemical synthesis and can be conjugated to a carrier
protein, if desired. Such commonly used carriers which are chemically coupled to the
polypeptide include keyhole limpet hemocyanin (KLH), thyroglobulin, bovine serum albumin
(BSA) and tetanus toxoid. The coupled polypeptide is then used to immunize the animal.
If desired, polyclonal or monoclonal antibodies can be further purified, for example by binding
to and elution from a matrix to which the polypeptide or a peptide to which the antibodies were
raised is bound. Those skilled in the art know various techniques common in immunology for
purification and/or concentration of polyclonal as well as monoclonal antibodies (Coligan et al,
Unit 9, Current Protocols in Immunology, Wiley Interscience, 1994).
Methods for making antibodies of all types, including fragments, are known in the art (See for
example, Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory,
New York (1988)). Methods of immunization, including all necessary steps of preparing the
immunogen in a suitable adjuvant, determining antibody binding, isolation of antibodies,
methods for obtaining monoclonal antibodies, and humanization of monoclonal antibodies are
all known to the skilled artisan
The antibodies may be humanized antibodies or human antibodies. Antibodies can be
humanized using a variety of techniques known in the art including CDR- grafting (EP239,400:
PCT publication WO.91/09967; U.S. patent Nos.5,225,539;5,530,101; and 5,585,089, veneering
or resurfacing (EP 592,106; EP 519,596; Padlan, Molecular Immunology 28(4/5):489-498
(1991); Studnicka et al., Protein Engineering 7(6):805-814 (1994); Roguska et al., PNAS
91:969-973 (1994)), and chain shuffling (U.S. Patent No. 5,565,332).
The monoclonal antibodies as defined include antibodies derived from one species (such as
murine, rabbit, goat, rat, human, etc.) as well as antibodies derived from two (or more) species,
such as chimeric and humanized antibodies.
Completely human antibodies are particularly desirable for therapeutic treatment of human
patients. Human antibodies can be made by a variety of methods known in the art including
phage display methods using antibody libraries derived from human immunoglobulin
sequences. See also U.S. Patent Nos. 4,444,887 and 4,716,111; and PCT publications WO
98/46645, WO 98/50433, WO 98/24893, WO 98/16654, WO 96/34096, WO 96/33735, and WO
91/10741, each of which is incorporated herein by reference in its entirety.
Additional information regarding all types of antibodies, including humanized antibodies,
human antibodies and antibody fragments can be found in WO 01/05998, which is incorporated
herein by reference in its entirety.
Neutralizing antibodies can be prepared by the methods discussed above, possibly with an
additional step of screening for neutralizing activity by, for example, a survival assay.
The terms "chemical compound", "small molecule", "chemical molecule" "small chemical
molecule" and "small chemical compound" are used interchangeably herein and are understood
to refer to chemical moieties of any particular type which may be synthetically produced or
obtained from natural sources and usually have a molecular weight of less than 2000 daltons,
less than 1000 daltons or even less than 600 daltons.
The present invention also relates to functional nucleic acids comprising a double-stranded
structure, their use for the manufacture of a medicament, a pharmaceutical composition
comprising such functional nucleic acids and a method for the treatment of a patient.
Hypoxia has been recognised as a key element in the pathomechanism of quite a number of
diseases such as stroke, emphysema and infarct which are associated with sub-optimum oxygen
availability and tissue damaging responses to the hypoxia conditions. In fast-growing tissues,
including tumor, a sub-optimum oxygen availability is compensated by undesired neoangiogenesis.
Therefore, at least in case of cancer diseases, the growth of vasculature is
undesired.
In view of this, the inhibition of angiogenesis and vascular growth, respectively, is subject to
intense research. Already today some compounds are available which inhibit undesired
angiogenesis and vascular growth. Some of the more prominent compounds are those inhibiting
VEGF and the VEGF receptor. In both cases, the effect of VEGF is avoided by either blocking
VEGF as such, for example by using an antibody directed against VEGF such as pursued by
Genentech's AVASTIN (monoclonal AB specific for VEGF) (Ferrara N.; Endocr Rev. 2004
Aug;25(4):581-611), or by blocking the corresponding receptor, i. e. the VEGF receptor
(Traxler P; Cancer Res. 2004 Jul 15;64(14):4931-41; or Stadler WM et al., Clin Cancer Res.
2004 May 15;10(10):3365-70).
As, however, angiogenesis and the growth of vasculature is a very basic and vital process in any
animal and human being, the effect of this kind of compound has to be focused at the particular
site where angiogenesis and vascular growth is actually undesired which renders appropriate
targeting or delivery a critical issue in connection with this kind of therapeutic approach.
It is thus an objective of the present invention to provide further means for the treatment of
diseases involving undesired growth of vasculature and angiogenesis, respectively.
By "small interfering RNA" (siRNA) is meant an RNA molecule which decreases or silences
(prevents) the expression of a gene/ mRNA of its endogenous cellular counterpart. The term is
understood to encompass "RNA interference" (RNAi). RNA interference (RNAi) refers to the
process of sequence-specific post transcriptional gene silencing in mammals mediated by small
interfering RNAs (siRNAs) (Fire et al, 1998, Nature 391. 806). The corresponding process in
plants is commonly referred to as specific post transcriptional gene silencing or RNA silencing
and is also referred to as quelling in fungi. The RNA interference response may feature an
endonuclease complex containing an siRNA, commonly referred to as an RNA-induced
silencing complex (RISC), which mediates cleavage of single-stranded RNA having sequence
complementary to the antisense strand of the siRNA duplex. Cleavage of the target RNA may
take place in the middle of the region complementary to the antisense strand of the siRNA
duplex (Elbashir et al 2001, Genes Dev., 15. 188). For recent information on these terms and
proposed mechanisms, see Bernstein E., Denli AM., Harmon GJ: The rest is silence. RNA. 2001
Nov;7(l 1):1509-21; and Nishikura K.: A short primer on RNAi: RNA-directed RNA polymerase
acts as a key catalyst. Cell. 2001 Nov 16;107(4):415-8. Examples of siRNA molecules which
may be used in the present invention are given in Tables A-C.
During recent years, RNAi has emerged as one of the most efficient methods for inactivation of
genes (Nature Reviews, 2002, v.3, p.737-47; Nature, 2002, v.418,p.244-51). As a method, it is
based on the ability of dsRNA species to enter a specific protein complex, where it is then
targeted to the complementary cellular RNA and specifically degrades it. In more detail,
dsRNAs are digested into short (17-29 bp) inhibitory RNAs (siRNAs) by type III RNAses
(DICER, Drosha, etc) (Nature, 2001, v.409, p.363-6; Nature, 2003, .425, p.415-9). These
fragments and complementary mRNA are recognized by the specific RISC protein complex.
The whole process is culminated by endonuclease cleavage of target mRNA (Nature Reviews,
2002, v.3, p.737-47; Curr Opin Mol Ther. 2003 Jun;5(3):217-24).
For disclosure on how to design and prepare siRNA to known genes see for example Chalk
AM, Wahlestedt C, Sonnhammer EL. Improved and automated prediction of effective siRNA
Biochem. Biophys. Res. Commun. 2004 Jun 18;319(l):264-74; Sioud M, Leirdal M., Potential
design rules and enzymatic synthesis of siRNAs, Methods Mol Biol.2004;252:457-69;
Levenkova N, Gu Q, Rux JJ.: Gene specific siRNA selector Bioinformatics. 2004 Feb
12;20(3):430-2. and Ui-Tei K, Naito Y, Takahashi F, Haraguchi T, Ohki-Hamazaki H, Juni A,
Ueda R, Saigo K., Guidelines for the selection of highly effective siRNA sequences for
mammalian and chick RNA interference Nucleic Acids Res. 2004 Feb 9;32(3):936-48. See also
Liu Y, Braasch DA, Nulf CJ, Corey DR. Efficient and isoform-selective inhibition of cellular
gene expression by peptide nucleic acids Biochemistry, 2004 Feb 24;43(7):1921-7. See also
PCT publications WO 2004/015107 (Atugen) and WO 02/44321 (Tuschl et al), and also Chiu
YL, Rana TM. siRNA function in RNAi: a chemical modification analysis, RNA 2003
Sep;9(9): 1034-48 and US Patent Nos.5898031 and 6107094 (Crooke) for production of
modified/ more stable siRNAs.
DNA-based vectors capable of generating siRNA within cells have been developed. The method
generally involves transcription of short hairpin RNAs that are efficiently processed to form
siRNAs within cells. Paddison et al. PNAS 2002, 99:1443-1448; Paddison et al. Genes & Dev
2002, 16:948-958; Sui et al. PNAS 2002, 8:5515-5520; and Brummelkamp et al. Science 2002,
296:550-553. These reports describe methods to generate siRNAs capable of specifically
targeting numerous endogenously and exogenously expressed genes.
For delivery of siRNAs, see, for example, Shen et al (FEES letters 539: 111-114 (2003)), Xia et
al., Nature Biotechnology 20: 1006-1010 (2002), Reich et al., Molecular Vision 9: 210-216
(2003), Sorensen et al. (J.Mol.Biol. 327: 761-766 (2003), Lewis et al., Nature Genetics 32: 107-
108 (2002) and Simeoni et al., Nucleic Acids Research 31, 11: 2717-2724 (2003). siRNA has
recently been successfully used for inhibition in primates; for further details see Tolentino et al.,
Retina 24(1) February 2004 pp 132-138.
siRNAs of the present invention
General specifications of siRNAs of the present invention
Generally, the siRNAs used in the present invention comprise a ribonucleic acid comprising a
double stranded structure, whereby the double- stranded structure comprises a first strand and a
second strand, whereby the first strand comprises a first stretch of contiguous nucleotides and
whereby said first stretch is at least partially complementary to a target nucleic acid, and the
second strand comprises a second stretch of contiguous nucleotides and whereby said second
stretch is at least partially identical to a target nucleic acid, whereby said first strand and/or said
second strand comprises a plurality of groups of modified nucleotides having a modification at
the 2'-position whereby within the strand each group of modified nucleotides is flanked on one or
both sides by a flanking group of nucleotides whereby the flanking nucleotides forming the
flanking group of nucleotides is either an unmodified nucleotide or a nucleotide having a
modification different from the modification of the modified nucleotides. Further, said first
strand and/or said second strand may comprise said plurality of modified nucleotides and may
comprises said plurality of groups of modified nucleotides.
The group of modified nucleotides and/or the group of flanking nucleotides may comprise a
number of nucleotides whereby the number is selected from the group comprising one nucleotide
to 10 nucleotides. In connection with any ranges specified herein it is to be understood that each
range discloses any individual integer between the respective figures used to define the range
including said two figures defining said range. In the present case the group thus comprises one
nucleotide, two nucleotides, three nucleotides, four nucleotides, five nucleotides, six nucleotides,
seven nucleotides, eight nucleotides, nine nucleotides and ten nucleotides.
The pattern of modified nucleotides of said first strand may be the same as the pattern of
modified nucleotides of said second strand, and may align with the pattern of said second strand.
Additionally, the pattern of said first strand may be shifted by one or more nucleotides relative to
the pattern of the second strand.
The modifications discussed above may be selected from the group comprising amino, fluoro,
methoxy, alkoxy and alky I.
The double stranded structure of the siRNA may be blunt ended, on one or both sides. More
specifically, the double stranded structure may be blunt ended on the double stranded structure's
side which is defined by the S'- end of the first strand and the 3'-end of the second strand, or the
double stranded structure may be blunt ended on the double stranded structure's side which is
defined by at the 3'-end of the first strand and the 5'-end of the second strand.
Additionally, at least one of the two strands may have an overhang of at least one nucleotide at
the 5'-end; the overhang may consist of at least one deoxyribonucleotide. At least one of the
strands may also optionally have an overhang of at least one nucleotide at the 3'-end.
The length of the double-stranded structure of the siRNA is typically from about 17 to 21 and
more preferably 18 or 19 bases. Further, the length of said first strand and/or the length of said
second strand may independently from each other be selected from the group comprising the
ranges of from about 15 to about 23 bases, 17 to 21 bases and 18 or 19 bases.
Additionally, the complementarily between said first strand and the target nucleic acid may be
perfect, or the duplex formed between the first strand and the target nucleic acid may comprise at
least 15 nucleotides wherein there is one mismatch or two mismatches between said first strand
and the target nucleic acid forming said double-stranded structure.
In some cases both the first strand and the second strand each comprise at least one group of
modified nucleotides and at least one flanking group of nucleotides, whereby each group of
modified nucleotides comprises at least one nucleotide and whereby each flanking group of
nucleotides comprising at least one nucleotide with each group of modified nucleotides of the
first strand being aligned with a flanking group of nucleotides on the second strand, whereby the
most terminal S' nucleotide of the first strand is a nucleotide of the group of modified
nucleotides, and the most terminal 3' nucleotide of the second strand is a nucleotide of the
flanking group of nucleotides. Each group of modified nucleotides may consist of a single
nucleotide and/or each flanking group of nucleotides may consist of a single nucleotide.
Additionally, it is possible that on the first strand the nucleotide forming the flanking group of
nucleotides is an unmodified nucleotide which is arranged in a 3' direction relative to the
nucleotide forming the group of modified nucleotides, and on the second strand the nucleotide
forming the group of modified nucleotides is a modified nucleotide which is arranged in 5'
direction relative to the nucleotide forming the flanking group of nucleotides.
Further the first strand of the siRNA may comprise eight to twelve, preferably nine to eleven,
groups of modified nucleotides, and the second strand may comprise seven to eleven, preferably
eight to ten, groups of modified nucleotides.
The first strand and the second strand may be linked by a loop structure, which may be
comprised of a non- nucleic acid polymer such as, inter alia, polyethylene glycol. Alternatively,
the loop structure may be comprised of a nucleic acid.
Further, the S'-terminus of the first strand of the siRNA may be linked to the 3'-terminus of the
second strand, or the 3'-end of the first strand may be linked to the S'-terminus of the second
strand, said linkage being via a nucleic acid linker typically having a length between 10-2000
nucleobases.
Particular specifications of siRNAs of the present invention
The invention provides a compound having the structure (structure A):
5' (N)x - Z 3' (antisense strand)
3'Z'-(N')y5' (sense strand)
wherein each N and N' is a ribonucleotide which may be modified or unmodified in its
sugar residue and (N)x and (N')y is oligomer in which each consecutive N or N' is joined
to the next N or N'by a covalent bond ;
wherein each of x and y is an integer between 19 and 40;
wherein each of Z and Z' may be present or absent, but if present is dTdT and is
covalently attached at the 3' terminus of the strand in which it is present;
and wherein the sequence of (N)x comprises an antisense sequence to cDNA of the
RTP801gene
In particular, the invention provides the above compound wherein the sequence of (N)x
comprises one or more of the antisense sequences present in Tables A, B and C.
In particular, the invention provides the above compound wherein the covalent bond is a
phosphodiester bond, wherein x = y, preferably wherein x = y = 19 , wherein Z and Z' are both
absent, wherein at least one ribonucleotide is modified in its sugar residue at the 2' position,
wherein the moiety at the 2' position is methoxy (2'-0-methyl) wherein alternating
ribonucleotides are modified in both the antisense and the sense strands and wherein the
ribonucleotides at the 5' and 3' termini of the antisense strand are modified in their sugar
residues, and the ribonucleotides at the 5' and 3' termini of the sense strand are unmodified in
their sugar residues.
In particular, the siRNA used in the present invention is an oligoribonucleotide wherein one
strand comprises consecutive nucleotides having, from 5' to 3', the sequence set forth in SEQ
ID NOS: 3-52 or in SEQ ID NOS: 103-174 or in SEQ ID NOS: 247-295 (which are sense
strands) wherein a plurality of the bases may be modified, preferably by a 2-O-methyl
modification, or a homolog thereof wherein in up to 2 of the nucleotides in each terminal region
a base is altered.
Further, the present invention provides for a method of treating a patient suffering from a
respiratory disorder, an eye disease, a microvascular disorder, or a spinal cord injury or disease
comprising administering to the patient a pharmaceutical composition comprising a compound
of the above structure (A) (having any of the specifics mentioned above) in a therapeutical ly
effective amount so as to thereby treat the patient. Additionally, the invention provides for the
use of a therapeutically effective amount of the above structure (A) (having any of the specifics
mentioned above) for the preparation of a medicament for promoting recovery in a patient
suffering from a respiratory disorder, an eye disease, a microvascular disorder or spinal cord
injury or disease.
An additional aspect of the present invention provides for a pharmaceutical composition
comprising a compound of the above structure (A) for the treatment of any of the diseases and
conditions mentioned herein.
Further, this aspect provides for a pharmaceutical composition comprising two or more
compounds of the above structure (A) for the treatment of any of the diseases and conditions
mentioned herein, whereby said two compounds may be physically mixed together in the
pharmaceutical composition in amounts which generate equal or otherwise beneficial activity, or
may be covalently or non-covalently bound, or joined together by a nucleic acid linker of a
length ranging from 2-100, preferably 2-50 or 2-30 nucleotides. Such siRNA molecules are
therefore comprised of a double-stranded nucleic acid structure as described herein, whereby
two siRNA sequences selected from Tables A-C and preferably from Table A, ID Nos: 14, 22,
23, 25, 27, 39, 41, 42, 49 and 50 are covalently or non-covalently bound or joined by a linker to
form a tandem siRNA molecule. Such tandem siRNA molecules comprising two siRNA
sequences would typically be of 38-150 nucleotides in length, more preferably 38 or 40- 60
nucleotides in length, and longer accordingly if more than two siRNA sequences are included in
the tandem molecule. A longer tandem molecule comprised of two or more longer sequences
which encode siRNA produced via internal cellular processing, e.g., long dsRNAs, is also
envisaged, as is a tandem molecule encoding two or more shRNAs. Such tandem molecules are
also considered to be a part of the present invention, and further information concerning them is
given below.
Said combined or tandem structures have the advantage that toxicity and/or off-target effects of
each siRNA are minimized, while the efficacy is increased.
In particular the siRNA used in the Examples has been such modified such that a 2' O-Me group
was present on the first, third, fifth, seventh, ninth, eleventh, thirteenth, fifteenth, seventeenth
and nineteenth nucleotide of the antisense strand, whereby the very same modification, i. e. a 2'-
O-Me group was present at the second, fourth, sixth, eighth, tenth, twelfth, fourteenth, sixteenth
and eighteenth nucleotide of the sense strand. Additionally, it is to be noted that the in case of
these particular nucleic acids according to the present invention the first stretch is identical to
the first strand and the second stretch is identical to the second strand and these nucleic acids are
also blunt ended. The siRNA was phosphorylated but it is envisaged that an un-phosphorylated
version may be simpler to prepare in large scale and said un-phosphorylated REDD 14, termed
REDD-14NP, was found to be just as biologically active as REDD-14 in a CNV model (see
Example 6). The sequence of this siRNA used in the experiments in Examples 6- 8 is that of
REDD 14, i.e., the sequence having internal reference No. 14 (see Table A).
The terminal region of the oligonucleotide refers to bases 1-4 and/or 16-19 in the 19-mer
sequences (Tables A and B below) and to bases 1-4 and/or 18-21 in the 21-mer sequences
(Table C beiow).
Additionally, the siRNAs used in the present invention are oligoribonucleotides wherein one
strand comprises consecutive nucleotides having, from 5' to 3', the sequence set forth SEQ ID
NOS: 53-102 or SEQ ID NOS: 175-246 or SEQ ID NOS: 296-344 (antisense strands) or a
homolog thereof wherein in up to 2 of the nucleotides in each terminal region a base is altered.
Thus, in particular aspects the oligonucleotide comprises a double-stranded structure, whereby
such double-stranded structure comprises a first strand and a second strand, whereby the first
strand comprises a first stretch of contiguous nucleotides and the second strand comprises a
second stretch of contiguous nucleotides, whereby the first stretch is either complementary or
identical to a nucleic acid sequence coding for gene RTP801 and whereby the second stretch is
either identical or complementary to a nucleic acid sequence coding for RTP801. Said first
stretch comprises at least 14 nucleotides, preferably at least 18 nucleotides and even more
preferably 19 nucleotides or even at least 21 nucleotides. In an embodiment the first stretch
comprises from about 14 to 40 nucleotides, preferably about 18 to 30 nucleotides, more
preferably from about 19 to 27 nucleotides and most preferably from about 19 to 23 nucleotides.
In an embodiment the second stretch comprises from about 14 to 40 nucleotides, preferably
about 18 to 30 nucleotides, more preferably from about 19 to 27 nucleotides and most preferably
from about 19 to 23 nucleotides or even about 19 to 21 nucleotides. In an embodiment the first
nucleotide of the first stretch corresponds to a nucleotide of the nucleic acid sequence coding for
RTP801, whereby the last nucleotide of the first stretch corresponds to a nucleotide of the
nucleic acid sequence coding for RTP801. In an embodiment the first stretch comprises a
sequence of at least 14 contiguous nucleotides of an oligonucleotide, whereby such
oligonucleotide is selected from the group comprising SEQ. ID. Nos. 3-344, preferably from the
group comprising the oligoribonucleotides of having the sequence of any of the serial numbers
14, 22, 23, 25, 27, 39, 41, 42, 49 and 50 in Table A. Additionally specifications of the siRNA
molecules used in the present invention may provide an oligoribonucleotide wherein the
dinucleotide dTdT is covalently attached to the 3' terminus, and/or in at least one nucleotide a
sugar residue is modified, possibly with a modification comprising a 2'-O-methyl modification.
Further, the 2' OH group may be replaced by a group or moiety selected from the group
comprising -H-OCH3) -OCH2CH3, -OCH2CH2 CH3, -NH2, and F. Further, the preferable
compounds of the present invention as disclosed above may be phosphorylated or nonphosphorylated.
Additionally, the siRNA used in the present invention may be an oligoribonucleotide wherein in
alternating nucleotides modified sugars are located in both strands. Particularly,, the
oligoribonucleotide may comprise one of the sense strands wherein the sugar is unmodified in
the terminal 5'and 3' nucleotides, or one of the antisense strands wherein the sugar is modified
in the terminal 5'and 3' nucleotides.
Additionally, further nucleic acids to be used in the present invention comprise at least 14
contiguous nucleotides of any one of the SEQ. ID. NO. 3 to 344, and more preferably 14
contiguous nucleotide base pairs at any end of the double-stranded structure comprised of the
first stretch and second stretch as described above. It will be understood by one skilled in the art
that given the potential length of the nucleic acid according to the present invention and
particularly of the individual stretches forming such nucleic acid according to the present
invention, some shifts relative to the coding sequence of the RTP801 gene as detailed in SEQ ID
NO:1 to each side is possible, whereby such shifts can be up to 1, 2, 3, 4, 5 and 6 nucleotides in
both directions, and whereby the thus generated double-stranded nucleic acid molecules shall
also be within the present invention.
An additional aspect of the present invention concerns a functional nucleic acid comprising a
double-stranded structure, whereby such double-stranded structure comprises
a first strand and a second strand, whereby
the first strand comprises a first stretch of contiguous nucleotides and the second strand
comprises a second stretch of contiguous nucleotides, whereby
the first stretch is either complementary or identical to a nucleic acid sequence coding for
RTP801 and whereby the second stretch is either identical or complementary to a nucleic
acid sequence coding for RTP801.
In an embodiment the nucleic acid is down-regulating RTP801, whereby the down-regulation of
RTP801 is selected from the group comprising down-regulation of RTP801 function, downregulation
of RTP801 protein and down-regulation of RTP801 mRNA expression.
In an embodiment the first stretch comprises at least 14 nucleotides, preferably at least 18
nucleotides and even more preferably 19 nucleotides.
In an embodiment the first stretch comprises from about 14 to 40 nucleotides, preferably about
18 to 30 nucleotides, more preferably from about 19 to 27 nucleotides and most preferably from
about 19 to 23 nucleotides.
In an embodiment the second stretch comprises from about 14 to 40 nucleotides, preferably
about 18 to 30 nucleotides, more preferably from about 19 to 27 nucleotides and most preferably
from about 19 to 23 nucleotides.
In an embodiment the first nucleotide of the first stretch corresponds to a nucleotide of the
nucleic acid sequence coding for RTP801, whereby the last nucleotide of the first stretch
corresponds to a nucleotide of the nucleic acid sequence coding for RTP801.
In an embodiment one stretch comprises a sequence of at least 14 contiguous nucleotides of a
nucleic acid sequence, whereby such nucleic acid sequence is selected from the sequences
disclosedi n Tables A-C, preferably from the group comprising SEQ. ID. NOs 53, 66, 67, 72,
73, 74, 75, 76, 77, 91, 92, 93, 94, 96, 101 and 102, more preferably selected from the group
comprising SEQ. ID. Nos 66, 75, 79, 91,94, 101 and 102, and most preferably selected from the
group comprising SEQ. ID. Nos 66, 74, 75 and 79.
In an embodiment the other stretch comprises a sequence of at least 14 contiguous nucleotides
of a nucleic acid sequence, whereby such nucleic acid sequence is selected from the sequences
disclosed! n Tables A-C, preferably from the group comprising SEQ. ID. NOs. 3, 16, 22, 23, 24,
25, 26, 27, 29, 41, 42, 43, 44, 45, 46, 51 and 52, more preferably selected from the group
comprising SEQ. ID. Nos 16, 24, 25, 29, 41, 44, 51, and 52, and most preferably selected from
the group comprising SEQ. ID. Nos 16,24,25 and 29.
In an embodiment
the first stretch has a sequence according to SEQ. ID. NO. 53 and the second stretch has
a sequence according to SEQ. ID. NO. 3;
the first stretch has a sequence according to SEQ. ID. NO. 66 and the second stretch has
a sequence according to SEQ. ID. NO. 16;
the first stretch has a sequence according to SEQ. ID. NO. 67 and the second stretch has
a sequence according to SEQ. ID. NO. 17;
the first stretch has a sequence according to SEQ. ID. NO. 72 and the second stretch has
a sequence according to SEQ. ID. NO. 22;
the first stretch has a sequence according to SEQ. ID. NO. 73 and the second stretch has
a sequence according to SEQ. ID. NO. 23;
the first stretch has a sequence according to SEQ. ID. NO. 74 and the second stretch has
a sequence according to SEQ. ID. NO. 24;
the first stretch has a sequence according to SEQ. ID. NO. 75 and the second stretch has
a sequence according to SEQ. ID. NO. 25;
the first stretch has a sequence according to SEQ. ID. NO. 76 and the second stretch has
a sequence according to SEQ. ID. NO. 26;
the first stretch has a sequence according to SEQ. ID. NO. 77 and the second stretch has
a sequence according to SEQ. ID. NO. 27;
the first stretch has a sequence according to SEQ. ID. NO. 79 and the second stretch has
a sequence according to SEQ. ID. NO. 29;
the first stretch has a sequence according to SEQ. ID. NO. 91 and the second stretch has
a sequence according to SEQ. ID. NO. 41;
the first stretch has a sequence according to SEQ. ID. NO. 92 and the second stretch has
a sequence according to SEQ. ID. NO. 42;
the first stretch has a sequence according to SEQ. ID. NO. 93 and the second stretch has
a sequence according to SEQ. ID. NO. 43;
the first stretch has a sequence according to SEQ. ID. NO. 94 and the second stretch has
a sequence according to SEQ. ID. NO. 44;
the first stretch has a sequence according to SEQ. ID. NO. 95 and the second stretch has
a sequence according to SEQ. ID. NO. 45;
the first stretch has a sequence according to SEQ. ID. NO. 96 and the second stretch has
a sequence according to SEQ. ID. NO. 46;
the first stretch has a sequence according to SEQ. ID. NO. 101 and the second stretch has
a sequence according to SEQ. ID. NO. 51; and
the first stretch has a sequence according to SEQ. ID. NO. 102 and the second stretch has
a sequence according to SEQ. ID. NO. 52.
In an embodiment the first stretch has a nucleic acid sequence which is selected from the group
comprising SEQ. ID. NO. 53, 66, 72, 73, 74, 75, 76, 77, 79, 91, 92, 93, 94, 95, 96, 101 and 102.
It is to be understood that while the terms "first" and "second" stretch are used in connection
with the nucleic acids of the present invention, they are used for the sake of convenience alone,
and any nucleic acid molecule of the invention that is described as having a first stretch with the
sequence X and a second stretch with the sequence Y, could also equally be described as having
a first stretch with the sequence Y and a second stretch with the sequence X, so long as it is
understood that one strech is comprised in the antisense strand, which must be antisense to a
portion of the coding sequence of the RTP801 gene, and the other strech is comprised! n the
sense strand, which must be complimentary (although not 100% complimentary) to the
antisense strand, all according o the definitions and specifications presented herein.
In an embodiment the first and/or the second strand comprises at least one overhang nucleotide
at the 3' end which is complementary or identical to the corresponding nucleotide of a nucleic
acid sequence coding for RTP801.
In an embodiment the first and/or the second strand comprises from 1 to 15 overhang
nucleotides at the 3' end, preferably the first and/or the second strand comprises from 1 to 10
overhang nucleotides at the 3' end, more preferably the first and/or the second strand comprises
from 1 to 5 overhang nucleotides at the 3' end, and most preferably the first and/or the second
strand comprises from 1 to 2 overhang nucleotides at the 3' end.
In an embodiment the first strand and/or the second strand comprises at least one overhang
nucleotide which is different from the corresponding nucleotide of the nucleic acid sequence
coding for RTP801.
In an embodiment the first strand comprises two overhang nucleotides which are different form
the corresponding nucleotide of a nucleic acid sequence coding for RTP801.
In an embodiment the first strand consists of the first stretch only.
In an embodiment the second strand consists of the second stretch only.
In an embodiment the first stretch and/or the first strand comprise(s) ribonucleotides.
In an embodiment the second stretch and/or the second strand comprise(s) ribonucleotides.
In an embodiment the first stretch and/or the second strand consist(s) of ribonucleotides.
In an embodiment some or all of the nucleotides are modified.
in a prcierreu emooaiment such modification is related to the nucleobase moiety of the
nucleotide, to the sugar moiety of the nucleotide and/or to the phosphate moiety of the
nucleotide.
In a more preferred embodiment the modification is a modification of a sugar moiety and the
modification is a modification at the 2' position, whereby the 2' OH group is replaced by a
group or moiety selected from the group comprising -H-OCHj, -OCH^CHj, -OCHzCHj CH3, -
NH2, and -F.
In an embodiment the modification is a modification of the nucleobase moiety and the
modification or modified nucleobase is selected from the group comprising inosine, xanthine,
hypoxanthine, 2-aminoadenine, 6-methyl, 2-propyl and other alkyladenines, 5-halo uracil, 5-
halocytosine, 5-halo cytosine, 6-azacytosine, 6-aza thymine, pseudo-uracil, 4-thiouracil, 8-haJo
adenine, 8-aminoadenine, 8-thiol ademne, 8-thiolalkyl adenines, 8-hydroxyl adenine and other
8-substituted adenines, 8-halo guanines, 8-amino guanine, 8-thiol guanine, 8-thioalkyl guanine,
8-hydroxylguanine and other substituted guanines, other aza- and deaza adenines, other aza- and
deaza guanines, 5-trifluoromethyl uracil and 5-trifluoro cytosine..
In an embodiment the modification is a modification of the phosphate moiety, whereby the
modified phosphate moiety is selected from the group comprising phosphothioate..
In an embodiment the first stretch and/or the second stretch comprises a plurality of groups of
modified nucleotides having a modification at the 2' position, whereby within the stretch each
group of modified nucleotides is flanked on one or both sides by a flanking group of
nucleotides, whereby the flanking nucleotides forming the flanking group of nucleotides are
either a non-modified nucleotide or a nucleotide having a modification different from the
modification of the modified nucleotides.
In a preferred embodiment the first stretch and/or the second stretch consists of ribonucleotides.
In a more preferred embodiment the first and the second stretch comprise a plurality of groups
of modified nucleotides.
In an embodiment the first stretch comprises said plurality of groups of modified nucleotides.
In an embodiment the second stretch comprises said plurality of groups of modified nucleotides.
In an embodiment each group of modified nucleotides and/or each group of flanking nucleotides
comprises a number of nucleotides, whereby the number is selected from the group comprising
one nucleotide to ten nucleotides.
In an embodiment the first stretch comprises a first pattern of modified nucleotides and the
second stretch comprises a second pattern of modified nucleotides.
In an embodiment the first pattern is the same pattern as the second pattern.
In another embodiment the first pattern aligns with the second pattern.
In a preferred embodiment the first pattern is shifted by one or more nucleotides relative to the
second pattern.
In an embodiment each of the groups of modified nucleotides consists of one modified
nucleotides and each of the groups of flanking nucleotides consists of one non-modified
nucleotide or a nucleotide having a modification which is different from the modification of the
modified nucleotides.
In a preferred embodiment the modified nucleotide has a -OMe group at the 2' position.
In a preferred embodiment the flanking nucleotide is a ribonucleotide which has a 2' OH
group.
In an embodiment the first stretch starts with a modified nucleotide at the 5' end and every other
nucleotide of the stretch is also a modified nucleotide, whereas a second nucleotide starting
from the 5' end and every other nucleotide is a non-modified nucleotide or a nucleotide having a
modification which is different from the modification of the modified nucleotide(s).
In an embodiment the first stretch is in antisense orientation to the nucleic acid sequence coding
forRTP801.
An additional aspect of the present invention related to a pharmaceutical composition
comprising a nucleic acid according to the first aspect of the present invention and/or a vector
according to the second aspect of the present invention and preferably a pharmaceutically
acceptable carrier; said composition optionally being for systemic or for local administration..
In an embodiment the composition is for the treatment of a disease, whereby the disease is
selected from the group comprising tumor diseases.
In an additional aspect, the problem underlying the present invention is solved by a method for
the prevention and/or treatment of a patient in need of such prevention and/or treatment
comprising the administration of a nucleic acid according to the present invention and/or vector
according to the present invention and/or a pharmaceutical composition according to the present
invention.
In an additional embodiment, a nucleic acid according to the present invention and/or a vector
according to the present invention are used for the manufacture of a medicament. The
medicament may be for the prevention and/or treatment of a disease, whereby such disease is
selected from the group comprising tumor diseases. The tumor disease may be selected from the
group comprising solid tumors, metastatic tumors including PTEN negative tumors, tumors
which are drug resistant and tumors where RTP801 inhibition can be used for sensitization.
Further, the tumor disease may be a late-stage tumor disease, or may involve cells which are
tumor suppressor negative; said tumor suppressor may be PTEN.
An additional aspect of the present invention is solved by a method for designing or screening a
nucleic acid which is suitable to down-regulate RTP80I, comprising the following steps:
a) designing or screening a nucleic acid which is suitable to down-regulate RTP801;
b) assessing defect of a nucleic acid according to any of the above aspects of the
present invention; and
c) comparing the effect of the nucleic acid of step a) with the effect of the nucleic
acid of step b).
In an embodiment the effect is the down-regulation of RTP801.
An additional aspect of the present invention is the use of a nucleic acid according to the present
invention as a sensitizer, particularly as a sensitizer in the treatment of a disease, whereby such
disease is preferably selected from the group comprising tumor and more particularly tumors
which are resistant to a treatment using chemotherapeutics and/or radiotherapeutics. Additional
diseases for which a nucleic acid of the present invention can serve as a sensitizer are disclosed
herein.
This application discloses that a nucleic acid comprising a double-stranded structure which is
specific for RTP801 is a suitable means of inhibiting angiogenesis/ growth of vasculature and
vascular leakage, (both from the existing vasculature and from growing vasculature). Additionally,
this application discloses (without being bound by theory) that RTP801 being a stress-inducible
protein (induced by hypoxia, oxidative stress, thermal stress, ER stress) is a factor acting in finetuning
of cell response to energy disbalance. Thus inhibition of RTP801 by such double-stranded
nucleic acid is suitable for treatment of any disease where cells should be rescued from apoptosis
due to stressful conditions (e.g. diseases accompanied by death of normal cells) or where cells
adapted to stressful conditions due to changes in RTP801 expression, should be killed (e.g. tumor
cells). In the latter case, upon inhibiting RTP801 through such double-stranded nucleic acid, this
survival factor with anti-apoptotic function in hypoxic cells, more particularly hypoxic cancer cells,
is made ineffective thus allowing the cells devoid of RTP801- mediated protection to be driven into
apoptosis. This can additionally occur when other apoptosis promoting factors are present Such
other apoptosis promoting factors include, among others, chemotherapy and radiation therapy. In
other words, the double-stranded nucleic acid according to the present invention may be effective
alone in cancer treatment (monotherapy) and also as a supplementary therapy.
Such double-stranded structure comprises a first strand and a second strand, whereby the first
strand comprises a first stretch of contiguous nucleotides and the second strand comprises a
second stretch of contiguous nucleotides, whereby the first stretch is either complementary or
identical to a nucleic acid sequence coding for RTP801 and whereby the second stretch is either
identical or complementary to a nucleic acid sequence coding for RTP801. By particularly using
RTP801 as a target for such kind of double-stranded nucleic acid, it is thus also possible to
immediately address a target in the cascade involved in the growth and development of
vasculature and angiogenesis, respectively, and thus in a different way compared to the pathway
used by VEGF inhibitors such as VEGF antibodies. Without wishing to be bound by any theory,
the present inventors assume that the nucleic acid according to the present invention may exert
its function in those cells which provide for a background which is involved in or observed in
connection with any disease where undesired, particularly hypoxia induced angiogenesis and/or
growth or development of vasculature occurs. This understanding is supported by the finding
that RTP801 knock-out mice do not exhibit any phenotype different from wildtype mice under
non-hypoxic conditions. Only upon induction of hypoxia as observed in a diseased condition
such as, e. g., tumor growth, the RTP801 related knock-out results in a pathology similar to the
one observed in humans suffering from this kind of disease.
It is to be understood that the nucleic acid according to the present invention is preferably a
functional nucleic acid. As used herein, the term functional nucleic acid preferably means a
nucleic acid the function of which is different from being active in the cell as a template for the
transcription of any hnRNA, mRNA, or any other transcription product, whereby either said
hnRNA, mRMA or any other transcription product, respectively, or the nucleic acid according to
the present invention is subject to a translation process, preferably a cellular translation process,
resulting in a biologically active RTP801 protein. It is to be acknowledged that a functional
nucleic acid as preferably used herein is capable of reducing the expression of a target nucleic
acid. More preferably, such reduction is based on a post-transcriptional gene silencing process
of the target nucleic acid. Even more preferably such reduction is based on RNA interference. A
most preferred form of the functional nucleic acid is an siRNA molecule or any further molecule
having the same effect as an siRNA molecule. Such further molecule is selected from the group
comprising siRNAs, synthetic siRNAs, shRNAs and synthetic shRNAs. As used herein siRNAs
may additionally comprise expression vector derived siRNAs, whereby the expression vector is
in a preferred embodiment a virus such as Adenoviruses, Adenoassociated viruses, Herpes
viruses and Lentiviruses. As used herein shRNA preferably means short hairpin RNAs. Such
shRNA can be made synthetically or can be generated using vector encoded expression systems,
preferably using RNA polymerase III promoters. In connection therewith it is to be
acknowledged that the functional nucleic acid according to the present invention is directed to
RTP801 which is also preferably referred to herein as the target and the nucleic acid coding for
said target as the target nucleic acid.
As preferably used herein, the double-stranded structure of the nucleic acid according to the
present invention .comprises any double-stranded structure, whereby such double-stranded
structure is preferably generated by the first stretch and the second stretch provided by the
nucleic acid having the basic design. The double-stranded structure may comprise one or several
mismatches. Such double-stranded structure is formed by Watson-Crick-base pairing and/or
Hoogsteen base pairing and/or similar base pairing mechanisms. Based on the basic design of
the nucleic acid according to the present invention it is preferred that one stretch, is in antisense
orientation to a nucleic acid sequence coding for RTP801 or a part thereof, whereas the other
stretch is in the sense orientation to a nucleic acid sequence coding for RTP801 or a part thereof.
Because of this, one stretch is complementary to a nucleic acid sequence coding for RTP801 or
a part thereof, and the other stretch is identical to a nucleic acid sequence coding for RTP801 or
a part thereof. In connection therewith it is to be acknowledged that the term identical, of
course, means also partially identical, whereby the identity, expressed as homology, is at least
80%, preferably 90%, more preferably 95%, 96%, 97%, 98%, 99% or 100%. Similar to the
definition of identity, complementarity can be defined in terms of homology, whereby such
homology is of the same range as the identity if the complementary strand would be translated
into the identical strand according to Watson-Crick base pairing rules. In an alternative
embodiment, one stretch is identical to a nucleic acid sequence coding for RTP801 or a part
thereof and the other stretch is complementary to a nucleic acid sequence coding for RTP801 or
a part thereof.
In a preferred embodiment, the nucleic acid according to the present invention is downregulating
RTP801 function. Down-regulation of RTP801 function preferably happens by
reduction in the level of expression at the protein level and/or the mRNA level, whereby such
reduced level of expression, preferably at the protein level, can be as little as 5% and be as high
as 100%, with reference to an expression under conditions where the nucleic acid according to
the present invention is not administered or is not functionally active. Such conditions are
preferably the conditions of or as present in an expression system, preferably an expression
system for RTP801. Such expression system is preferably a translation system which can be an
in vitro translation system, more preferably a cell, organ and/or organism. It is more preferred
that the organism is a multicellular organism, more preferably a mammal, whereby such
mammal is preferably selected from the group comprising man, monkey, mouse, rat, guinea pig,
rabbit, cat, dog, sheep, cow, horse, cattle and pig. In connection with the down-regulation it is to
be acknowledged that said down-regulation may be a function of time, i. e. the down-regulation
effect is not necessarily observed immediately upon administration or functional activation of
the nucleic acids according to the present invention, but may be deferred in time as well as in
space, i. e. in various cells, tissues and/or organs. Such deferment may range from 5%-100%,
preferably 10 to 50%. It will be acknowledged by the ones skilled in the art that a 5 % reduction
for a longer time period might be as effective as a 100% reduction over a shorter time period. It
will also be acknowledged by the ones skilled in the art that such deferment strongly depends on
the particular functional nucleic acid actually used, as well as on the target cell population and
thus, ultimately, on the disease to be treated and/or prevented according to the technical teaching
of the present application, insofar, a 5 % reduction-over a longer time period~might be as
effective as 100% reduction over a shorter time period. It will also be acknowledged by the ones
skilled in the art that the deferment can occur at any level as outlined above, i.e. a deferment in
function, whereby such function is any function exhibited by RTP801, a deferment in protein
expression or a deferment at mRNA expression level.
In a preferred embodiment the first stretch comprises at least 14 nucleotides, preferably 14
contiguous nucleotides. It will be acknowledged by the one skilled in the art that the first stretch
should have a length which is suitable to allow for specifically addressing a nucleic acid
sequence coding for RTP801 and more specifically the nucleic acid coding for RTP801 as
present in the translation system where the expression of RTP801 is to be reduced. Again
without wishing to be bound by any theory or any mode of action of the nucleic acid according
to the present invention, it seems that there is an interaction between the nucleic acid according
to the present invention and the nucleic acid sequence coding for RTP801, preferably at the
transcript level, i. e. upon generation of an mRNA from the respective nucleic acid sequence
coding for RTP801. Due to the likelihood of any sequence of the nucleic acid according to the
present invention being identical to or complementary to a sequence contained in the genome or
transcriptome of the translation system, the length of the first stretch should thus be as long as to
make sure that, under the assumption that some kind of base pairing between the nucleic acid
coding for RTP801 and one of the strands of the nucleic acid according to the present invention
actually occurs, only the sequence coding for RTP801 but no other coding sequence, preferably
no other essential coding sequence, of the genome or the transcriptome is addressed for or by
such base pairing. By this length, the occurrence of off-target effects can be reduced and
preferably eliminated. To increase the stringency of this kind of specifically addressing RTP801
and the nucleic acid sequence coding therefor, the first stretch preferably has a length of at least
18 or 19 nucleotides. The upper limit for the length of the first stretch is preferably less than 50
nucleotides, however, the length can be significantly longer and can comprise 100, 200 or even
500 nucleotides or any length in-between. Apart from this, one skilled in the art will prefer to
have a rather short first stretch, particularly in case the nucleic acid according to the present
invention is chemically synthesised as the shorter the sequence is, the less time and material
consuming the synthesis thereof will be and the lower will be the rate at which incorrect
nucleotides are inserted into the respective sequence.-Another factor which is to be taken into
consideration in connection with fixing the length of the first stretch is the fact that, typically at
a length beyond 50 or more nucleotides, an unspecific interferon response may be observed. It
depends on the particular condition to be treated whether this kind of unspecific interferon
response is to be tolerated or not. For example, an interferon response could be tolerated if the
interferon response and/or the expression of the interferon genes can be limited to the
pathogenic cells.
In view of this, more preferred lengths of the first stretch are from about 14 to 40 nucleotides, 18
to 30 nucleotides, 19 to 27 nucleotides, 21 to 25 nucleotides and 19 to 23 nucleotides.
The same considerations as outlined above for the first stretch are applicable to the second
stretch which may thus comprise any length as described herein in connection with the first
stretch. It is also within the present invention that the length of the first stretch is different from
the length of the second stretch, however, it is preferred that both stretches have the same
length.
According to the basic design of the nucleic acid, the first stretch and second stretch are parts of
the first strand and second strand, respectively, of the nucleic acid according to the present
invention. It will be acknowledged that at either end, i. e. at the 5' end as well as the 3' end the
first strand and/or second strand may comprise one or several nucleotides, preferably additional
nucleotides, at any combination.
In connection therewith it is to be acknowledged that those nucleotides of the individual strand
going beyond the end(s) of the stretch corresponding to the respective strand can be used to
further contribute to the complementarity and identity, respectively, of the stretch and thus to the
specific addressing of the nucleic acid sequence coding for RTP801.
It will be acknowledged that, basically, based on the technical teaching provided herein, the
nucleic acid according to the present invention can address any part of the nucleic acid sequence
coding for RTP801, preferably coding for RTP801 in the translation system where the
expression of RTP801 is to be reduced. Insofar, the present invention comprises any nucleic
acid having the characteristics as defined herein, whereby the complementary and identical
strands and stretches of the nucleic acid according to the present invention can basically start
from any nucleotide of the nucleic acid sequence coding for RTP801. Accordingly, under the
proviso that the first stretch of the nucleic acid according to the present invention is
complementary to the nucleic acid sequence coding for RTP801, i. e. is the antisense strand
thereof or is in antisense orientation thereto, the first nucleotide of said stretch, i. e. the most 5'
terminal nucleotide corresponds, i. e. aligns to the last nucleotide of the sequence coding for
RTP801 at the 3' end. In a further embodiment such most 5' terminal nucleotide corresponds to
the penultimate nucleotide of the nucleic acid coding for RTP801 and so on until the last
position is reached which, given the length of the antisense stretch, still allows that the antisense
strand of the nucleic acid according to the present invention is complementary to the nucleic
acid sequence coding for RTP801. Insofar, any nucleic acid according to the present invention is
within the present invention which could be generated by scanning the nucleic acid sequence
coding for RTP801 starting from the most 5' terminal nucleotide thereof and laying over the
basic design of the nucleic acid according to the present invention and realising the
characteristics for such nucleic acid according to the present invention. The same considerations
are applicable to the embodiments disclosed herein where the complementarity and identity of
the nucleic acid according to the present invention is not only provided by the first stretch and
second stretch, respectively, but such complementarity and identity also involves one or more
nucleotides beyond the first stretch and second stretch, respectively, then being part of the first
strand and second strand, respectively.
Of the various nucleic acids according to the present invention as disclosed herein, those with
internal reference numbers 14, 22, 23, 25, 27, 39, 41, 42, 49 and 50 (see Table A) are
particularly preferred. In connection therewith it is to be noted that those nucleic acids according
to the present invention which can be used in both human and an animal model such as rat
and/or mouse are particularly useful. The surprising advantage of these particular nucleic acids
according to the present invention resides in the fact that they are effective both in human and in
an animal model which means that the test results obtained in the animal model can be
immediately transferred from the animal model to the human being and more particularly
without the necessity to make any changes to the human sequence which would otherwise
become necessary in case the nucleic acid according to the present invention was designed such
as to comprise (a) sequence(s) which differ(s) between the species, more particularly the species
used for animal model testing and man as the ultimate preferred organisms or patient. It is
further preferred that these nucleic acids have a modification pattern as also described in the
examples.
However, it is also within the present invention that any of the sequences according to SEQ. ID.
NOs. 3, 16-17, 22-27, 29, 41-46, 51-53, 66-67, 72-77, 79, 91-96 and 101-102 and respective
combinations resulting in the nucleic acid molecules according to the present invention having
internal reference numbers 14, 22, 23, 25, 27, 39, 41, 42, 49 and 50, is only partially contained
in a further nucleic acid according to the present invention. Preferably, the further nucleic acids
according to the present invention comprise at least 14 contiguous nucleotides of the SEQ. ID.
NO.s 3, 16-17, 22-27, 29, 41-46, 51-53, 66-67, 72-77, 79, 91-96 and 101-102, and more
preferably 14 contiguous nucleotide base pairs at any end of the double-stranded structure
comprised of the first stretch and second stretch as outlined in the preceding table. It will be
understood by the ones skilled in the art that given the potential length of the nucleic acid
according to the present invention and particularly of the individual stretches forming such
nucleic acid according to the present invention, some shifts relative to the coding sequence of
RTP801 to each side is possible, whereby such shifts can be up to 1, 2, 3, 4, 5 and 6 nucleotides
in both directions, and whereby the thus generated double-stranded nucleic acid molecules shall
also be within the present invention.
In a preferred embodiment of the present invention the first stretch and the first strand have the
same length. Likewise it is preferred that the second strand has the same length as the second
stretch, whereby it is even more preferred that the first stretch and the second stretch have the
same length. In a still more preferred embodiment, the first strand only comprises the first
stretch and the second strand only comprises the second stretch. In an even more preferred
embodiment neither the first stretch, and thus the first strand, nor the second stretch, and thus
the second strand, comprise an overhang. In other words, it is also within the present invention
that the double-stranded nucleic acids according to the present invention are blunt ended,
preferably at each end of the double-stranded structure of the nucleic acids according to the
present invention. Such blunt ended structure can be realized in connection with any other
embodiments of the nucleic acids according to the present invention, particularly those
embodiments where the nucleic acids according to the present invention have a modification
pattern, more preferably a modification pattern as described herein.
In a further aspect, the nucleic acid according to the present invention has thus a basic design
which provides for blunt ends at both ends of the double-stranded structure of the nucleic acid
according to the present invention. However, it is also within the present invention that there is a
overhang, i. e. a stretch of one or more nucleotides protruding from the double-stranded
structure. The overhang can be, in principle, at the 5' end of the antisense strand, at the 3' end of
the antisense strand, at the 5' end of the sense strand and/or the 3' end of the sense strand. It is
V
to be noted that realising any single of said options as well as any combination thereof is within
the present invention. More preferred is a combination, whereby the overhang is located at the
3' end of the antisense strand and at the 3' end of the sense strand. It is also within the present
invention that the overhang is at the 5' end of the antisense strand and at the 5' end of the sense
strand. Furthermore it is within the present invention that the overhang is located only at the
antisense strand of double-stranded structure, more preferably at the 3' end of the antisense
strand of the double-stranded structure.
In connection with the overhangs, it is to be noted that the overhang plus the stretch preferably
form the strand and the lengths provided for the stretches herein apply also to these
embodiments. The individual overhang can, independent of its location, consist of at least one
nucleotide. However, the individual overhang can comprise as many as 10 and is preferably two
nucleotides long. It is within the present invention that the respective nucleotide(s) forming the
overhang(s) is/are also complementary to the nucleic acid sequence coding for RTP801 in case
of the first strand being complementary to said nucleic acid sequence coding for RTP801, and
the overhang being at the 3' or 5' end of the antisense strand, or that the overhang(s) is/are
identical to the nucleic acid sequence coding for RTP801 in case the first strand is identical to
the nucleic acid sequence coding for RTP801. The same applies to any overhang located at the
second stretch of the basic design of the nucleic acid according to the present invention,
whereby it is to be acknowledged that the overhang design at the second stretch can be
independent from the overhang design of the first stretch.
It is also within the present invention that the overhang forming nucleotides are neither
complementary nor identical to the corresponding nucleotides of the nucleic acid sequence
coding for RTP801. As used herein, and preferably in this embodiment, "corresponding" means
the respective nucleotides which follow at the 5' end and/or the 3' end of the stretch having a
nucleotide counterpart on the nucleic acid coding for RTP801.
Preferably, the first strand comprises at its 3' end two nucleotides, preferably deoxynucleotides
and more preferably two TT and/or this kind of nucleotides also at the 3' end of the second
strand, whereby more preferably the length of the first stretch and the second stretch is 19
nucleotides. The strands are thus comprised of the stretch and the overhang. In this
embodiment the double-stranded structure consists of 19 base pairs and an overhang of two
nucleotides at each end of 3' end of the individual stretch.
In a preferred embodiment, the first stretch and/or the first strand comprise(s) ribonucleotides,
whereby it is particularly preferred that the first stretch consists in its entirety of ribonucleotides.
The same applies to the second stretch and the second strand, respectively. In connection
therewith, however, each and any of the nucleotides of the first stretch and second stretch,
respectively, is modified in a preferred embodiment. The same applies to the first strand and
second strand, respectively. Particularly the terminal nucleotides, irrespective whether they are
ribonucleotides or deoxyribonucleotides, can have an OH-group which as such can be modified.
Such OH-group may stem from either the sugar moiety of the nucleotide, more preferably from
the 5'position in case of the 5'OH-group and/or from the 3'position in case of the 3'OH-group,
or from a phosphate group attached to the sugar moiety of the respective terminal nucleotide.
The phosphate group may in principle be attached to any OH-group of the sugar moiety of the
nucleotide. Preferably, the phosphate group is attached to the 5'OH-group of the sugar moiety in
case of the free 5'OH-group and/or to the 3'OH-group of the sugar moiety in case of the free
3 'OH-group still providing what is referred to herein as free 5' or 3' OH-group.
As used herein with any strategy for the design of RNAi or any embodiment of RNAi disclosed
herein, the term end modification means a chemical entity added to the most 5' or 3' nucleotide
of the first and/or second strand. Examples for such end modifications include, but are not
limited to, 3' or 5' phosphate, inverted (deoxy) abasics, amino, fluoro, chloro, bromo, CN, CF,
methoxy, imidazole, caboxylate, thioate, C| to CIQ lower alkyl, substituted lower alkyl, alkaryl
or aralkyl, OCF3, OCN, O-, S-, or N-alkyl; O-, S-, or N-alkenyl; SOCH3; SO2CH3; ONO2; NO2,
N3; heterocycloalkyi; heterocycloalkaryl; aminoalkylamino; polyalkylamino or substituted silyl,
as, among others, described in European patents EP 0 586 520 B1 or EP 0 618 925 Bl.
As used herein, alkyl or any term comprising "alkyl" preferably means any carbon atom chain
comprising 1 to 12, preferably 1 to 6 and more, preferably 1 to 2 C atoms.
A further end modification is a biotin group. Such biotin group may preferably be attached to
either the most 5' or the most 3' nucleotide of the first and/or second strand or to both ends. In a
more preferred embodiment the biotin group is coupled to a polypeptide or a protein. It is also
within the scope of the present invention that the polypeptide or protein is attached through any
of the other aforementioned end modifications. The polypeptide or protein may confer further
characteristics to the nucleic acid molecules according to the present invention. Among others
the polypeptide or protein may act as a ligand to another molecule. If said other molecule is a
receptor the receptor's function and activity may be activated by the binding ligand. The
receptor may show an internalization activity which allows an effective transfection of the
ligand bound nucleic acid molecules according to the present invention. An example for the
ligand to be coupled to the inventive nucleic acid molecule is VEGF and the corresponding
receptor is the VEGF receptor.
Various possible embodiments of the RNAi of the present invention having different kinds of
end modification(s) are presented in the following table 1.
TABLE 1: VARIOUS EMBODIMENTS OF THE INTERFERING RIBONUCLEIC ACID
(Table Removed)
The various end modifications as disclosed herein are preferably located at the ribose moiety of
a nucleotide of the nucleic acid according to the present invention. More particularly, the end
modification may be attached to or replace any of the OH-groups of the ribose moiety, including
but not limited to the 2'OH, 3'OH and 5'OH position, provided that the nucleotide thus
modified is a terminal nucleotide. Inverted abasics are nucleotides, either desoxyribonucleotides
or ribonucleotides which do not have a nucleobase moiety. This kind of compound is, among
others, described in Sternberger, M., Schmiedeknecht, A., Kretschmer, A., Gebhardt, F.,
Leenders, F., Czauderna, F., Von Carlowitz, I., Engle, M., Giese, K., Beigelman, L. & Klippel,
A. (2002). Antisense Nucleic Acid Drug Dev, 12, 131-43
Any of the aforementioned end modifications may be used in connection with the various
embodiments of RNAi depicted in Table 1; it is to be noted that the 51 end modifications
mentioned above are usually only presenti in the sense strand of the siRNA molecule
Further modifications can be related to the nucleobase moiety, the sugar moiety or the
phosphate moiety of the individual nucleotide.
Such modification of the nucleobase moiety can be such that the derivatives of adenine,
guanine, cytosine and thymidine and uracil, respectively, are modified. Particularly preferred
modified nucleobases are selected from the group comprising inosine, xanthine, hypoxanthine,
2-aminoadenine, 6-methyl, 2-propyl and other alkyladenines, 5-halo uracil, 5-halocytosine, 5-
halo cytosine, 6-azacytosine, 6-aza thymine, pseudo-uracil, 4-thiouracil, 8-halo adenine, 8-
aminoadenine, 8-thiol adenine, 8-thiolalkyl adenines, 8-hydroxyl adenine and other 8-
substituted adenines, 8-halo guanines, 8-amino guanine, 8-thiol guanine, 8-thioalkyl guanine, 8-
hydroxylguanine and other substituted guanines, other aza- and deaza adenines, other aza- and
deaza guanines, 5-trifluoromethyl uracil and 5-trifluoro cytosine.
In another preferred embodiment, the sugar moiety of the nucleotide is modified, whereby such
modification preferably is at the 2' position of the ribose and desoxyribose moiety, respectively,
of the nucleotide. More preferably, the 2' OH group is replaced by a group or moiety selected
from the group comprising amino, fluoro, alkoxy and alkyl. Preferably, alkoxy is either methoxy
or ethoxy. Also preferably alkyl means methyl, ethyl, propyl, isobutyl, butyl and isobutyl. It is
even more preferred that, regardless of the type of modification, the nucleotide is preferably a
ribonucleotide.
The modification of the phosphate moiety is preferably selected from the group comprising
phosphothioates.
It will be acknowledged by the one skilled in the art that the nucleic acid of the present
invention which consists of a multitude of nucleotides may thus be formed by nucleotides which
are linked through a phosphodiester linkage or through a phosphothioate linkage, or a
combination of both along the length of the nucleotide sequence of the individual strand and
stretch, respectively.
A further form of nucleotides used may actually be siNA which is, among others, described in
international patent application WO 03/070918.
The nucleotides forming the first stretch and first strand, respectively, of the nucleic acid
according to the present invention can comprise one or more modified nucleotides, whereby the
individual modified nucleotide has a modification which is preferably a modification as
disclosed herein. In addition to the particular modification, the modification can be or comprise
some sort of label, whereby the label is selected from the group chemiluminescent labels,
fluorescent labels and radio labels. These kinds of labels are known to the one skilled in the art
and, e. g., described in Ausubel et al., Current Protocols in Molecular Biology, John Wiley and
Sons, Baltimore, Maryland, 1998. The thus labelled nucleic acid according to the present
invention may be used also for diagnostic purposes or for monitoring the site of action as well as
for the staging of any treatment, preferably related to any of the diseases disclosed herein.
In a preferred embodiment, the nucleic acid according to the present invention is modified such
that the pyrimidine nucleotides in the sense stretch or strand are 2' O-methyl pyrimidine
nucleotides and, either additionally or alternatively, the purine nucleotides in the sense stretch or
strand are 2'-deoxypurine nucleotides. In a further embodiment the pyrimidine nucleotides
present in the sense stretch or sense strand are 2'-deoxy-2'-fluoro pyrimidine nucleotides.
In an alternative embodiment, the modification is not based on the chemistry of the nucleotide, i.
e. the modification depends on whether the nucleotide to be modified is either a purine
nucleotide or a pyrimidine nucleotide, but is predominantly based on the individual nucleotide's
spatial arrangement in the overall double-stranded structure of the basic design of the nucleic
acid according to the present invention.
More particularly, either the first strand and first stretch, respectively, or the second strand and
second stretch, respectively, show a spatial pattern of modification of the nucleotides forming
said stretches and strands, respectively.
Focusing on the first stretch first, there is a pattern of groups of modified nueleotides and groups
of non-modified nucleotides. These groups of non-modified nucleotides are also referred to
herein as flanking groups of nucleotides. More preferably, the pattern consists of groups of
modified nucleotides and non-modified nucleotides. Even more preferably, the pattern is a
regular pattern and even more preferably an alternating pattern along the length of the first
stretch of the nucleic acid according to the present invention. The group of modified nucleotides
may either consist of one or of several nucleotides which are modified and which are preferably
nucleotides which are modified at the 2' position, i. e. have a modification at the sugar moiety.
More preferably, this modification is a 2'-O-Me modification.
The group of non-modified nucleotides may either consist of one or of several nucleotides
which are either not modified, whereby the not-modified nucleotides are preferably
nbonucleotides, or the not modified nucleotides are nucleotides having a modification, whereby
such modification is different from the modification shown by the nucleotides forming the
group of modified nucleotides. Even more preferably, the not modified nucleotides are
ribonucleotides. It is to be noted that the term not modified and non-modified nucleotide are
used in an interchangeable manner if not indicated to the contrary. The first stretch of the
nucleic acid according to the present invention may either start with a group of modified
nucleotides or start with a group of non-modified nucleotides as defined herein. However, it is
preferred that the first stretch starts with a group of modified nucleotides. Most preferably, the
group of modified nucleotides consists of a single nucleotide. In connection with this
embodiment the first stretch is preferably in antisense orientation to the nucleic acid coding for
RTP801. It is also within the present invention that the modification as exhibited by the
nucleotides forming the group of modified nucleotides is the same for all groups of modified
nucleotides present on the first stretch. However, it is also within the present invention that
some group of modified nucleotides have a different modification than one or several groups of
modified nucleotides present on the first stretch.
On the second strand of the nucleic acid according to the present invention, a pattern as
described for the first stretch can also be realised. The same characteristics as described in
connection with the first stretch can be realized in an embodiment on the second stretch as well,
whereby it is preferred that, under the proviso that the second stretch is in sense orientation
relative to the nucleic acid sequence coding for RTP801, the second strand of the nucleic acid
according to the present invention starts with a group of non-modified nucleotides.
The nucleic acid according to the present invention comprising a double-stranded structure may
comprise a first stretch having the modification pattern as described herein. Alternatively, the
double-stranded nucleic acid according to the present invention may comprise a second stretch
having the modification pattern as outlined above. It is, however, most preferred that the doublestranded
nucleic acid according to the present invention consists of a first stretch and a second
stretch, whereby both the first stretch and the second stretch have a spatial modification pattern
as described herein.
It is within the present invention that the characteristics of the spatial modification pattern is the
same on both stretches in terms of size of the groups of modified nucleotides and groups of nonmodified
nucleotides and the kind of modifications actually used. Preferably, the spatial pattern
of modification on the first stretch is shifted such that a group of modified nucleotides on the
first stretch is opposing a group of non-modified nucleotides on the second stretch and vice
versa. However, it is also with the present invention that the patterns are exactly aligned, i. e.
that a group of modified nucleotides on the first stretch is opposing a group of non-modified
nucleotides on the second stretch and a group of non-modified nucleotides on the first stretch is
opposing a group of non-modified nucleotides on the second stretch. It is still within the present
invention that the spatial pattern of modification on the first stretch and the second stretch is
shifted relative to each other so that only a first portion of a group of modified nucleotides on
one stretch is opposing a portion of a group of non-modified nucleotides on the other stretch,
whereas the second portion of the group of modified nucleotides is opposing another group of
modified nucleotides. It is within the present invention that the disclosure provided herein on the
spatial modification pattern of the stretch(es) of the nucleic acid according to the present
invention applies also to the strand(s) of the nucleic acid according to the present invention.
However, it is preferred that the stretches of the nucleic acid comprise the spatial modification
pattern and the strands comprise such stretches and one or more overhang(s) as disclosed herein.
It is particularly preferred that the overhang is a phosphate group at the 3' end of either the
antisense strand, or the sense strand or both strands, whereby it is more preferred that the
phosphate group is at the 3' end of both the antisense strand and the sense strand. In an even
more preferred embodiment, the phosphate group is a phosphate group as defined herein.
It is also within the present invention that the nucleic acid according to the present invention
may exhibit a linker connecting the first and the second strand. Such linker is preferably a
polymer. The polymer can be any synthetic or natural polymer. Possible synthetic linkers are,
among others, PEG or a polynucleotide. Such linker is preferably designed such as to allow the
either partial or complete folding back of the first stretch onto the second stretch and vice versa.
Finally, it is within the present invention that the nucleic acid according to the present invention
is a synthetic one, a chemically synthesised one, an isolated one, or one derived from any
natural sources such as, for example, prepared by means of recombinant technology. In
connection with the preparation of any nucleic acid according to the present invention any
modification as disclosed herein can be introduced either prior, during or subsequent to the
preparation of the respective nucleic acid according to the present invention as known to the
ones skilled in the art.
The vector according to the present invention comprises a nucleic acid according to the present
invention. Additionally, the vector may include elements to control targeting, expression and
transcription of said nucleic acid in a cell selective manner as is known in the art. The plasmid
can include a promoter for controlling transcription of the heterologous material, i. e. the nucleic
acid according to the present invention, and can be either a constitutive or an inducible promoter
to allow selective transcription. Enhancers that may be required to obtain necessary transcription
levels can optionally be included. Enhancers are generally any non-translated DNA sequences
which work contiguously with the coding sequence, thus in cis, to change the basal transcription
level dictated by the promoter. The expression of such constructs is known to the one skilled in
the art and may be done, e. g., by providing a respective tandem construct or by having different
promoters transcribing for the first and second strand and first and second stretch, respectively,
of the nucleic acid according to the present invention.
When the nucleic acid according to the present invention is manufactured or expressed,
preferably expressed in vivo, more preferably in a patient who is in need of the nucleic acid
according to the present invention, such manufacture or expression preferably uses an
expression vector, preferably a mammalian expression vector. Expression vectors are known in
the art and preferably comprise plasmids, cosmids, viral expression systems. Preferred viral
expression systems include, but are not limited to, adenovirus, retrovirus and lentivirus.
Methods are known in the art to introduce the vectors into cells or tissues. Such methods can be
found generally described in Sambrook et al., Molecular cloning: A Laboratory Manual, Cold
Springs Harbour Laboratory, New York (1983, 1992), or in Ausubel et al., Current Protocols in
Molecular Biology, John Wiley and Sons, Baltimore, Maryland, 1998.
Suitable methods comprise, among others, transfection, lipofection, electroporation and
infection with recombinant viral vectors. In connection with the present invention, an additional
feature of the vector is in one embodiment an expression limiting feature such as a promoter and
regulatory element, respectively, that are specific for the desired cell type thus allowing the
expression of the nucleic acid sequence according to the present invention only once the
background is provided which allows the desired expression.
In a further aspect the present invention is related to a pharmaceutical composition comprising a
nucleic acid according to the present invention and/or a vector according to the present
invention and, optionally, a pharmaceutically acceptable carrier, diluent or adjuvants or other
vehicle(s). Preferably, such carrier, diluents, adjuvants and vehicles are inert, and non-toxic. The
pharmaceutical composition is in its various embodiments adapted for administration in various
ways. Such administration comprises systemic and local administration as well as oral,
subcutaneous, parenteral, intravenous, intraarterial, intramuscular, intraperitonial, intranasal, and
intrategral.
It will be acknowledged by the ones skilled in the art that the amount of the pharmaceutical
composition and the respective nucleic acid and vector, respectively, depends on the clinical
condition of the individual patient, the site and method of administration, scheduling of
administration, patient age, sex, bodyweight and other factors known to medical practitioners.
The pharmaceutically effective amount for purposes of prevention and/or treatment is thus
determined by such considerations as are known in the medical arts. Preferably, the amount is
effective to achieve improvement including but limited to improve the diseased condition or to
provide for a more rapid recovery, improvement or elimination of symptoms and other
indicators as are selected as appropriate measures by those skilled in the medical arts.
In a preferred embodiment, the pharmaceutical composition according to the present invention
may comprise other pharmaceutically active compounds. Preferably, such other
pharmaceutically active compounds are selected from the group comprising compounds which
allow for uptake intracellular cell delivery, compounds which allow for endosomal release,
compounds which allow for, longer circulation time and compounds which allow for targeting
of endothelial cells or pathogenic cells. Preferred compounds for endosomal release are
chloroquine, and inhibitors of ATP dependent H+ pumps.
The pharmaceutical composition is preferably formulated so as to provide for a single dosage
administration or a multi-dosage administration.
It will be acknowledged that the pharmaceutical composition according to the present invention
can be used for any disease which involves undesired development or growth of vasculature
including angiogenesis, as well as any of the diseases and conditions described herein.
Preferably, these kind of diseases are tumor diseases. Among tumor diseases, the following
rumors are most preferred: endometrial cancer, colorectal carcinomas, gliomas, endometrial
cancers, adenocarcinomas, endometrial hyperplasias, Cowden's syndrome, hereditary nonpolyposis
colorectal carcinoma, Li-Fraumene's syndrome, breast-ovarian cancer, prostate cancer
(Ali, I. U., Journal of the National Cancer Institute, Vol. 92, no. 11, June 07, 2000, page 861 -
863), Bannayan-Zonana syndrome, LDD (Lhermitte-Duklos' syndrome) (Macleod, K., supra)
hamartoma-macrocephaly diseases including Cow disease (CD) and Bannayan-Ruvalcaba-Rily
syndrome (BRR), mucocutaneous lesions (e. g. trichilemmonmas), macrocephaly, mental
retardation, gastrointestinal harmatomas, lipomas, thyroid adenomas, fibrocystic disease of the
breast, cerebellar dysplastic gangliocytoma and breast and thyroid malignancies (Vazquez, F.,
Sellers, W. R., supra).
It is to be acknowledged that any of the tumor disease to be treated with the pharmaceutical
composition according to the present invention is preferably a late stage tumor disease. In
another embodiment, the tumor disease involves cells which are tumor suppressor negative,
whereby more preferably the tumor suppressor is PTEN.
The pharmaceutical composition according to the present invention can also be used in a method
for preventing and/or treating a disease as disclosed herein, whereby the method comprises the
administration of a nucleic acid according to the present invention, a vector according to the
present invention or a pharmaceutical composition or medicament according to the present
invention for any of the diseases described herein.
In a further aspect, the present invention is related to a method for designing or screening a
nucleic acid which is suitable to down-regulate RTP801, more particularly to down-regulate
RTP801 function. This method comprises the use of a nucleic acid sequence as disclosed herein
and the assessment of such nucleic acid in a suitable assay. Such assay is known in the art and,
for example, described in the example part of this application. In a further step, a doublestranded
nucleic acid is designed, preferably according to the design principles as laid down
herein, which is suitable to down-regulate RTP801, preferably in connection with a post
transcriptional gene silencing mechanism such as RNA interference. Also the thus obtained, i. e.
designed or screened, nucleic acid is assessed in the respective assay and the result, i. e. the
effect of both the nucleic acid according to the present invention as well as the newly designed
or screened nucleic acid in such assay compared. Preferably, the designed or screened nucleic
acid is more suitable in case it is either more stable or more effective, preferably both. It will be
acknowledged that the method will be particularly effective if any of the nucleic acids according
to the present invention is used as a starting point. It is thus within the present invention that
new nucleic acid molecules will be designed based on the principles disclosed herein, whereby
the target sequence on the RTP801 mRNA will be slightly shifted relative to the target sequence
on the RTP801 mRNA for the corresponding nucleic acid according to the present invention.
Preferably the new nucleic acid will be shifted by at least one or more nucleotides relative to the
stretch on the target mRNA in either the 5' or the 3' direction of the mRNA coding for RTP801.
It is however with in the present invention that the shift occurs in both directions simultaneously
which means that the new nucleic acid incorporates the nucleic acid according to the present
invention used as a starting point. It is also within the present invention that the elongation of
the nucleic acid according to the present invention and used as a starting point is biased to either
the 3' end or the 5' end. In case of such as bias either the 3' end or the 5' end of the new nucleic
acid is longer, i.e more extended than the other end. When the new nucleic acid molecule is
generated by extending either the 3' end of the 5' end of the antisense strand and/or the sense
strand, the following sequence of steps is typically applied. If the shift is to the 5' end of the
mRNA of RTP801, the 3' end of the antisense strand has to be extended by the number of the
nucleotides by which the 5' end of the mRNA of RTP801 is shifted. The nucleotide(s) thus to be
added to the 3' end of the antisense strand of the new nucleic acid is/are complementary to those
nucleotides following at the 5' end of the target sequence on the RTP801 mRNA used for the
nucleic acid molecule according to the present invention used as a starting point. The same has
to be done to the sense strand. However the nucleotides to be added to the sense strand have to
correspond, i.e. be complementary to the nucleotides newly added to the 3' end of the antisense
strand which means that they have to be added to the 5' end of the sense strand. The latter step
on the sense strand, however has to be done only to the extent that apart from the antisense
strand also the sense strand shall be shifted, which is the case in preferred embodiments of the
present invention. Although this shifting can be done to an extent defined by the ones skilled in
the art, more preferably the shift shall be done such that also the new nucleic acid still contains a
strech of at least 14 nucleotides, preferably 14 contiguous nucleotides as exhibited by any of the
nucleic acid molecules disclosed herein.
The synthesis of any of the nucleic acids described herein is within the skills of the one of the
art. Such synthesis is, among others, described in Beaucage S.L. and Iyer R.P., Tetrahedron
1992; 48: 2223-2311, Beaucage S.L. and Iyer R.P., Tetrahedron 1993; 49: 6123-6194 and
Caruthers M.H. et. al., Methods Enzymol. 1987; 154: 287-313, the synthesis of thioates is,
among others, described in Eckstein F., Annu. Rev. Biochem. 1985; 54: 367-402, the synthesis
of RNA molecules is described in Sproat B., in Humana Press 2005 Edited by Herdewijn P.;
Kap. 2: 17-31 and respective downstream processes are, among others, described in Pingoud A.
et. al., in 1RL Press 1989 Edited by Oliver R.W.A.; Kap. 7: 183-208 and Sproat B., in Humana
Press 2005 Edited by Herdewijn P.; Kap. 2: 17-31 (supra).
siRNA for RTP801 can be made using methods known in the art as described above, based on
the known sequence of RTP801 (SEQ ID NO:1), and can be made stable by various
modifications as described above. For further information, see Example 9.
Further, in relation to the methods of the present invention as described herein, additional RNA
molecules may be used with said methods e.g. inhibitory RNA molecules of the present
invention include single stranded oligoribonucleotides preferably comprising stretches of at least
7-10 consecutive nucleotides present in the sequences detailed in Tables A-C,
said oligoribonucleotides being capable of forming [and/or comprising] double stranded regions
in particular conformations that are recognized by intracellular complexes, leading to the
degradation of said oligoribonucleotides into smaller RNA molecules that are capable of
exerting inhibition of their corresponding endogenous gene, and DNA molecules encoding such
RNA molecules. The corresponding endogenous gene is preferably the 801 gene and may
additionally be the VEGF gene and /or the VEGF-Rlgene. The invention also provides a
composition comprising the above single stranded oligoribonucleotide in a carrier, preferably a
pharmaceutical ly acceptable carrier.
Additionally, the present invention provides for combination therapy for all the conditions
disclosed herein and in particular conditions involving choroidal neovascularization. In said
combination therapy, both the RTP801 and VEGFR genes are inhibited in order to ameliorate
the symptoms of the disease being treated. These genes may be inhibited with a combination of
siRNAs or antibodies (including aptamer antibodies) or both. The present invention therefore
also provides for a novel pharmaceutical composition comprising an RTP801 inhibitor and a
VEGF or VEGFR-1 inhibitor, the RTP801 inhibitor preferable being an siRNA, more preferably
an siRNA molecule detailed in Tables A-C and in particular, siRNA Nos: 14, 22, 23, 25, 27, 39,
41, 42, 49 and 50 of Table A, and the VEGF/ VEGFR-1 inhibitor optionally being an antibody
or aptamer. The combined use of said compounds (i.e., RTP801 siRNA and VEGF antibody or
any other combined example disclosed herein) in the preparation of a medicament is also part of
the present invention.
Thus, RTP801 siRNA such as an siRNA molecule detailed in Tables A-C and in particular,
siRNA Nos: 14, 22, 23, 25, 27, 39, 41, 42, 49 and 50 of Table A may be administered in
conjunction with agents which target VEGF or VEGF receptor 1 (VEGFR1). Such agents
currently exist on the market or in various stages of approval and work through different
mechanisms. Antibodies and antibody fragments such as ranibizumab (Lucentis, Genentech)
attach to released VEGF to inhibit binding of VEGF to active receptors. An aptamer which can
act like a ligand/antibody (Macugen, Eyetech/Pfizer, approved recently by the FDA for wet
AMD) is also a possibility. Macugen bonds with extracellular VEGF to block its activity. These
drugs are administered locally by intravitreal injection. Anti-VEGF siRNA based compounds
(such as Acuity's CandS inhibitor of VEGF or SIRNA's 027 inhibitor of VEGFR-1) are also
available. Additionally, the small molecule aminosterol Squalamine (Genaera) which is
administered systemically reportedly interferes in multiple facets of the angiogenic process,
including inhibiting VEGF and other growth factor signaling in endothelial cells.
The conjoined administration of an RTP801 inhibitor, preferably an siRNA, and any of the
above VEGF / VEGFR-1 inhibitory agents can have a synergistic effect whereby said combined
treatment is more effective than treatment by any of these individual compositions, irrespective
of dosage in the single therapy option. This synergistic effect is also supported by preliminary
results obtained by the Asignee, as detailed in Example 6.
RTPSOli has a different mechanism of action and is potentially synergistic with VEGF-VEGFR
inhibitors. A study in RTP801 KO mice indicates that protective phenotype in the KO mice
persists in spite of the fact that expression of VEGF mRNA in the eye is as high as in the WT
mice. Our additional preliminary data indicate that inhibition of RTP801 may be synergistic
with the inhibition of VEGF-VEGFR regulatory axis in treatment of retinal pathology. The
inventors of the present invention have found in appropriate experiments that administration of
siRNA against RTP801 in the model of AMD (see Example 6 below) leads not only to
downregulation of RTP801 itself but also, as a consequence, to upregulation of the
antiangiogenic and neuroprotective factor PEDF as well as the downregulation of expression of
MCP1, a macrophage chemoattractant protein. Thus, inhibition of RTP801 simultaneously
confers antiangiogenic, neuroprotective and anti-inflammatory effects.
It is to be understood that, in the context of the present invention, any of the siRNA molecules
disclosed herein, or any long double-stranded RNA molecules (typically 25-500 nucleotides in
length) which are processed by endogenous cellular complexes (such as DICER - see above) to
form the siRNA molecules disclosed herein, or molecules which comprise the siRNA molecules
disclosed herein, can be employed in the treatment of the diseases or disorders described herein.
Additional disorders which can be treated by the molecules and compositions of the present
invention include all types of choroidal neovascularization (CNV), which occurs not only in wet
AMD but also in other ocular pathologies such as ocular histoplasmosis syndrome, angiod
streaks, ruptures in Bruch's membrane, myopic degeneration, ocular tumors and some retinal
degenerative diseases.
An additional aspect of the present invention provides for methods of treating an apoptosis related
disease. Methods for therapy of diseases or disorders associated with uncontrolled, pathological
cell growth, e.g. cancer, psoriasis, autoimmune diseases, inter alia, and methods for therapy of
diseases associated with ischemia and lack of proper blood flow, e.g. myocardial infarction (MI)
and stroke, are provided. "Cancer" or "Tumor" refers to an uncontrolled growing mass of abnormal
cells. These terms include both primary tumors, which may be benign or malignant, as well as
secondary tumors, or metastases which have spread to other sites in the body. Examples of cancertype
diseases include, inter alia: carcinoma (e.g.: breast, colon and lung), leukemia such as B cell
leukemia, lymphoma such as B-cell lymphoma, blastema such as neuroblastoma and melanoma.
The invention also provides a composition comprising one or more of the compounds of the
invention in a carrier, preferably a pharmaceutically acceptable carrier. This composition may
comprise a mixture of two or more siRNAs for different genes or different siRNAs for the same
gene. A composition comprising siRNA for the RTP801 gene and siRNA for the VEGF gene
and /or the VEGF-R1 gene is envisaged.
Another compound of the invention comprises the above compound of the invention (structure
A) covalently or non-covalently bound to one or more compounds of the invention (structure
A). This compound may be delivered in a carrier, preferably a pharmaceutically acceptable
carrier, and may be processed intracellularly by endogenous cellular complexes to produce one
or more siRNAs of the invention. Another compound of the invention comprises the above
compound of the invention (structure A) covalently or non-covalently bound to an siRNA for
another gene, especially the VEGF gene and/or the VEGF-R1 gene.
This invention also comprises a novel chemical entity which is an RTP801 inhibitor, preferably
an siRNA, chemically bound, covalently or non-covalently, to any of the above VEGF /
VEGFR-1 inhibitory agents. A particular chemical entity envisaged is an siRNA RTP801
inhibitor covalently bound to an antibody to VEGF or VEGF receptor-1. Methods of production
of such novel chemical entities are known to those skilled in the art.
This invention also comprises a tandem double-stranded structure which comprises two or more
siRNA sequences, which is processed intracellularly to form two or more different siRNAs, one
inhibiting 801 and a second inhibiting VEGF / VEGFR-1 In a related aspect, this invention
also comprises a tandem double-stranded structure which comprises two or more siRNA
sequences, which is degraded intracellularly to form two or more different siRNAs, both
inhibiting 801.
In particular, it is envisaged that a long oligonucleotide (typically about 80-500 nucleotides in
length) comprising one or more stem and loop structures, where stem regions comprise the
sequences of the oligonucleotides of the invention, may be delivered in a carrier, preferably a
pharmaceutically acceptable carrier, and may be processed intracellularly by endogenous
cellular complexes (e.g. by DROSHA and DICER as described above) to produce one or more
smaller double stranded oligonucleotides (siRNAs) which are oligonucleotides of the invention.
This oligonucleotide can be termed a tandem shRNA construct. It is envisaged that this long
oligonucleotide is a single stranded oligonucleotide comprising one or more stem and loop
structures, wherein each stem region comprises a sense and corresponding antisense siRNA
sequence of an 801 gene. In particular, it is envisaged that this oligonucleotide comprises sense
and antisense siRNA sequences as depicted in any one of Tables A through C. Alternatively, the
tandem shRNA construct may comprise sense and corresponding antisense siRNA sequence of
an 801 gene and additionally sense and corresponding antisense siRNA sequence of a different
gene such as VEGF or VEGF-R1.
As mentioned herein, siRNA against RTP801 may be the main active component in a
pharmaceutical composition, or may be one active component of a pharmaceutical composition
containing two or more siRNAs (or molecules which encode or endogenously produce two or
more siRNAs, be it a mixture of molecules or one or more tandem molecule which encodes two
or more siRNAs), said pharmaceutical composition further being comprised of one or more
additional siRNA molecule which targets one or more additional gene. Simultaneous inhibition
of RTP801 and said additional gene(s) will probably have an additive or synergistic effect for
treatment of the diseases disclosed herein, according to the following:
Acute Renal Failure (ARF) and other microvascular disorders: the pharmaceutical composition
for treatment of ARF may be comprised of the following compound combinations: 1)
RTP801 siRNA and p53 siRNA dimers; 2) RTP801 and Fas siRNA dimers; 3) RTP801 and Bax
siRNA dimers; 4) p53 and Fas siRNA dimers; 5) RTP801 and Bax siRNA dimers; 6) RTP801
and Noxa siRNA dimers; 7) RTP801 and Puma siRNA dimers; 8) RTP801 (REDD1) and
RTP801L (REDD2) siRNA dimmers; 9) RTP801 siRNA, Fas siRNA and any of RTP801L
siRNA p53 siRNA, Bax siRNA, Noxa siRNA or Puma siRNA to form trimers or polymers (i.e.,
tandem molecules which encode three siRNAs).
Macular degeneration (MD), diabetic retinopathy (DR), spinal cord injury: pharmaceutical
compositions for treatment of MD, DR and spinal cord injury may be comprised of the
following compound combinations: 1) RTP801 siRNA combined with either of VEGF siRNA,
VEGF-R1 siRNA, VEGF R2 siRNA, PKCbeta siRNA, MCP1 siRNA, eNOS siRNA, KLF2
siRNA, RTP801L siRNA (either physically mixed or in a tandem molecule); 2) RTP801 siRNA
in combination with two or more siRNAs of the above list (physically mixed or in a tandem
molecule encodimg three siRNAs, or a combination thereof).
COPD and respiratory disorders: the pharmaceutical composition for treatment of respiratory
disorders may be comprised of the following compound combinations: RTP801 siRNA
combined with siRNA against one or more of the following genes: elastases, matrix
metalloproteases, phospholipases, caspases, sphingomyelinase, and ceramide synthase.
Additionally, RTP801 siRNA or any nucleic acid molecule comprising or encoding RTP801
siRNA can be linked (covalently or non-covalently) to antibodies, in order to achieve enhanced
targeting for treatment of the diseases disclosed herein, according to the following:
ARF: anti-Fas antibody (preferably neutralizingantibodies).
Macular degeneration, diabetic retinopathy, spinal cord injury: anti-Fas antibody, anti-MCPl
antibody, anti-VEGFRl and anti-VEGFR2 antibody. The antibodies should be preferably be
neutralizing antibodies.
Any molecules, such as, for example, antisense DNA molecules which comprise the siRNA
sequences disclosed herein (with the appropriate nucleic acid modifications) are particularly
desirable and may be used in the same capacity as their corresponding siRNAs for all uses and
methods disclosed herein.
The invention also comprises a method of treating a patient suffering from a disorder such as the
disorders described herein comprising administering to the patient the above composition or
compound in a therapeutically effective dose so as to thereby treat the patient.
By the term "antisense" (AS) or "antisense fragment" is meant a polynucleotide fragment
(coprising either deoxyribonucleotides, ribonucleotides or a mixture of both) having inhibitory
antisense activity, said activity causing a decrease in the expression of the endogenous genomic
copy of the corresponding gene (in this case RTP801). An RTP801 AS polynucleotide is a
polynucleotide which comprises consecutive nucleotides having a sequence of sufficient length
and homology to a sequence present within the sequence of the RTP801 gene set forth in SEQ
ID NO: 1 to permit hybridization of the AS to the gene. The sequence of the AS is designed to
complement a target mRNA of interest and form an RNA:AS duplex. This duplex formation can
prevent processing, splicing, transport or translation of the relevant mRNA. Moreover, certain
AS nucleotide sequences can elicit cellular RNase H activity when hybridized with their target
mRNA, resulting in mRNA degradation (Calabretta et al, 1996: Antisense strategies in the
treatment ofleukemias. Semin Oncol. 23(l):78-87). In that case, RNase H will cleave the RNA
component of the duplex and can potentially release the AS to further hybridize with additional
molecules of the target RNA. An additional mode of action results from the interaction of AS
with genomic DNA to form a triple helix which can be transcriptionally inactive. Particular AS
fragments are the AS of the DNA encoding the particular fragments of RTP801 described
herein.
Many reviews have covered the main aspects of antisense (AS) technology and its therapeutic
potential (Wright &Anazodo, 1995. Antisense Molecules and Their Potential For The
Treatment Of Cancer and AIDS. Cancer J. 8:185-189.'). There are reviews on the chemical
(Crooke, 1995. Progress in antisense therapeutics, Hematol. Pathol. 2:59; Uhlmann and
Peyman, 1990. Antisense Oligomicleotides: A New Therapeutic Principle. Chem Rev 90(4): 543-
584.), cellular (Wagner, 1994. Gene inhibition using antisense oligodeoxynucleotides. Nature
372:333.) and therapeutic (Hanania, et al 1995. Recent advances in the application of gene
therapy to human disease. Am. J. Med. 99:537.; Scanlon et al., 1995. Oligonucleotides-mediated
modulation of mammalian gene expression. FASEB J. 9:1288.; Gewirtz, 1993.
Oligodeoxynucleotide-based therapeutics for human leukemias, Stem Cells Dayt. 11:96.)
aspects of this technology.
Antisense intervention in the expression of specific genes can be achieved by the use of
synthetic AS oligonucleotide sequences (see Lefebvre-d'Hellencourt et al, 1995.
Jmmunomodulation by cytokine antisense oligonucleotides. Eur. Cytokine Netw. 6:7.\ Agrawal,
1996. Antisense oligonucleotides: towards clinical trials, TJBTECH, 14:376.; Lev-Lehman et
al., 1997. Antisense Oligomers in vitro and in vivo. In Antisense Therapeutics, A. Cohen andS.
Smicek, eds (Plenum Press, New York)). AS oligonucleotide sequences are designed to
complement a target mRNA of interest and form an RNA:AS duplex. This duplex formation can
prevent processing, splicing, transport or translation of the relevant mRNA. Moreover, certain
AS nucleotide sequences can elicit cellular RNase H activity when hybridized with their target
mRNA, resulting in mRNA degradation (Calabretta, et al, 1996. Antisense strategies in the
treatment ofleukemias. Semin. Oncol. 23:78.). In that case, RNase H will cleave the RNA
component of the duplex and can potentially release the AS to further hybridize with additional
molecules of the target RNA. An additional mode of action results from the interaction of AS
with genomic DNA to form a triple helix which may be transcriptionally inactive.
The sequence target segment for the antisense oligonucleotide is selected such that the sequence
exhibits suitable energy related characteristics important for oligonucleotide duplex formation
with their complementary templates, and shows a low potential for self-dimerization or selfcomplementation
(Anazodo et al., 1996). For example, the computer program OLIGO (Primer
Analysis Software, Version 3.4), can be used to determine antisense sequence melting
temperature, free energy properties, and to estimate potential self-dimer formation and selfcomplimentary
properties. The program allows the determination of a qualitative estimation of
these two parameters (potential self-dimer formation and self-complimentary) and provides an
indication of "no potential" or "some potential" or "essentially complete potential". Using this
program target segments are generally selected that have estimates of no potential in these

parameters. However, segments can be used that have "some potential" in one of the categories.
A balance of the parameters is used in the selection as is known in the art. Further, the
oligonucleotides are also selected as needed so that analogue substitution do not substantially
affect function.
Phosphorothioate antisense oligonucleotides do not normally show significant toxicity at
concentrations that are effective and exhibit sufficient pharmacodynamic half-lives in animals
(Agrawal, 1996. Antisense oligonucleotides: towards clinical trials, TIBTECH, 14:376.) and are
nuclease resistant. Antisense induced loss-of-function phenotypes related with cellular
development have been shown for the glial fibrillary acidic protein (GFAP), for the
establishment of tectal plate formation in chick (Galileo et al., 1991. J. Cell. Biol., 112:1285.)
and for the N-myc protein, responsible for the maintenance of cellular heterogeneity in
neuroectodermal cultures (ephithelial vs. neuroblastic cells, which differ in their colony forming
abilities, rumorigenicity and adherence) (Rosolen et al., 1990. Cancer Res. 50:6316.; Whitesell
et al., 1991. Episome-generated N-myc antisense RNA restricts the differentiation potential of
primitive neuroectodermal cell lines. Mol. Cell. Biol. 11:1360.). Antisense oligonucleotide
inhibition of basic fibroblast growth factor (bFgF), having mitogenic and angiogenic properties,
suppressed 80% of growth in glioma cells (Morrison, 1991. Suppression of basic fibroblast
growth factor expression by antisense oligonucleotides inhibits the growth of transformed
human astrocytes. J. Biol. Chem. 266:728.) in a saturable and specific manner. Being
hydrophobic, antisense oligonucleotides interact well with phospholipid membranes (Akhter et
al, 1991. Interactions of antisense DNA oligonucleotide analogs with phospholipid membranes
(liposomes) Nuc. Res. 19:5551-5559.). Following their interaction with the cellular plasma
membrane, they are actively (or passively) transported into living cells (Loke et al, 1989.
Characterization of oligonucleotide transport into living cells. PNAS USA 86:3474.), in a
saturable mechanism predicted to involve specific receptors (Yakubov et al, 1989. PNAS USA
86:6454.).
A "ribozyme" is an RNA molecule that possesses RNA catalytic ability (see Cech for review)
and cleaves a specific site in a target RNA.
In accordance with the present invention, ribozymes which cleave RTP801 mRNA may be
utilized as RTP801 inhibitors. This may be necessary in cases where antisense therapy is limited
by stoichiometric considerations (Sarver et al., 1990, Gene Regulation and Aids, pp. 305-325).
Ribozymes can then be used that will target the RTP801 sequence. The number of RNA
molecules that are cleaved by a ribozyme is greater than the number predicted by
stochiochemistry. (Hampel and Tritz, 1989; Uhlenbeck, 1987).
Ribozymes catalyze the phosphodiester bond cleavage of RNA. Several ribozyme structural
families have been identified including Group I introns, RNase P, the hepatitis delta virus
ribozyme, hammerhead ribozymes and the hairpin ribozyme originally derived from the
negative strand of the tobacco ringspot virus satellite RNA (sTRSV) (Sullivan, 1994; U.S. Pat.
No. 5,225,347, columns 4-5). The latter two families are derived from viroids and virusoids, in
which the ribozyme is believed to separate monomers from oligomers created during rolling
circle replication (Symons, 1989 and 1992). Hammerhead and hairpin ribozyme motifs are most
commonly adapted for trans-cleavage of mRNAs for gene therapy (Sullivan, 1994). The
ribozyme type utilized in the present invention is selected as is Known in the art. Hairpin
ribozymes are now in clinical trial and are the preferred type. In general the ribozyme is from
30-100 nucleotides in length. Delivery of ribozymes is similar to that of AS fragments and/or
siRNA molecules.
It will be noted that all the polynucleotides to be used in the present invention may undergo
modifications so as to possess improved therapeutic properties. Modifications or analogs of
nucleotides can be introduced to improve the therapeutic properties of polynucleotides.
Improved properties include increased nuclease resistance and/or increased ability to permeate
cell membranes. Nuclease resistance, where needed, is provided by any method known in the art
that does not interfere with biological activity of the AS polynucleotide, siRNA, cDNA and/or
ribozymes as needed for the method of use and delivery (Iyer et al., 1990; Eckstein, 1985;
Spitzer and Eckstein, 1988; Woolf et al., 1990; Shaw et al., 1991). Modifications that can be
made to oligonucleotides in order to enhance nuclease resistance include modifying the
phophorous or oxygen heteroatom in the phosphate backbone. These include preparing methyl
phosphonates, phosphorothioates, phosphorodithioates and morpholino oligomers. In one
embodiment it is provided by having phosphorothioate bonds linking between the four to six 3'-
terminus nucleotide bases. Alternatively, phosphorothioate bonds link all the nucleotide bases.
Other modifications known in the art may be used where the biological activity is retained, but
the stability to nucleases is substantially increased.
All analogues of, or modifications to, a polynucleotide may be employed with the present
invention, provided that said analogue or modification does not substantially affect the function
of the polynucleotide. The nucleotides can be selected from naturally occurring or synthetic
modified bases. Naturally occurring bases include adenine, guanine, cytosine, thymine and
uracil. Modified bases of nucleotides include inosine, xanthine, hypoxanthine, 2- aminoadenine,
6-methyl, 2-propyl and other alkyl adenines, 5-halo uracil, 5-halo cytosine, 6-aza cytosine and
6-aza thymine, psuedo uracil, 4- thiuracil, 8-halo adenine, 8-aminoadenine, 8-thiol adenine, 8-
thiolalkyl adenines, 8-hydroxyl adenine and other 8-substituted adenines, 8-halo guanines, 8-
amino guanine, 8-thiol guanine, 8-thioalkyl guanines, 8- hydroxyl guanine and other substituted
guanines, other aza and deaza adenines, other aza and deaza guanines, 5-trifluoromethyl uracil
and 5- trifluoro cytosine.
In addition, analogues of polynucleotides can be prepared wherein the structure of the
nucleotide is fundamentally altered and that are better suited as therapeutic or experimental
reagents. An example of a nucleotide analogue is a peptide nucleic acid (PNA) wherein the
deoxyribose (or ribose) phosphate backbone in DNA (or RNA is replaced with a polyamide
backbone which is similar to that found in peptides. PNA analogues have been shown to be
resistant to degradation by enzymes and to have extended lives in vivo and in vitro. Further,
PNAs have been shown to bind stronger to a complementary DNA sequence than a DNA
molecule. This observation is attributed to the lack of charge repulsion between the PNA strand
and the DNA strand. Other modifications that can be made to oligonucleotides include polymer
backbones, cyclic backbones, or acyclic backbones.
The polypeptides employed in the present invention may also be modified, optionally
chemically modified, in order to improve their therapeutic activity. "Chemically modified" -
when referring to the polypeptides, means a polypeptide where at least one of its amino acid
residues is modified either by natural processes, such as processing or other post-translational
modifications, or by chemical modification techniques which are well known in the art. Among
the numerous known modifications typical, but not exclusive examples include: acetylation,
acylation, amidation, ADP-ribosylation, glycosylation, GPI anchor formation, covalent
attachment of a lipid or lipid derivative, methylation, myristlyation, pegylation, prenylation,
phosphorylation, ubiqutination, or any similar process.
Additional possible polypeptide modifications (such as those resulting from nucleic acid
sequence alteration) include the following:
"Conservative substitution" - refers to the substitution of an amino acid in one class by an amino
acid of the same class, where a class is defined by common physicochemical amino acid side
chain properties and high substitution frequencies in homologous polypeptides found in nature,
as determined, for example, by a standard Dayhoff frequency exchange matrix or BLOSUM
matrix. Six general classes of amino acid side chains have been categorized and include: Class I
(Cys); Class II (Ser, Thr, Pro, Ala, Gly); Class III (Asn, Asp, Gin, Glu); Class IV (His, Arg,
Lys); Class V (He, Leu, Val, Met); and Class VI (Phe, Tyr, Tip). For example, substitution of an
Asp for another class III residue such as Asn, Gin, or Glu, is a conservative substitution.
"Non-conservative substitution" - refers to the substitution of an amino acid in one class with an
amino acid from another class; for example, substitution of an Ala, a class II residue, with a
class III residue such as Asp, Asn, Glu, or Gin.
"Deletion" - is a change in either nucleotide or amino acid sequence in which one or more
nucleotides or amino acid residues, respectively, are absent.
"Insertion" or "addition" - is that change in a nucleotide or amino acid sequence which has
resulted in the addition of one or more nucleotides or amino acid residues, respectively, as
compared to the naturally occurring sequence.
"Substitution" - replacement of one or more nucleotides or amino acids by different nucleotides
or amino acids, respectively. As regards amino acid sequences the substitution may be
conservative or non- conservative.
In an additional embodiment of the present invention, the RTP801 polypeptide or
polynucleotide may be used to diagnose or detect macular degeneration in a subject. A detection
method would typically comprise assaying for RTP801 mRNA or RTP801 polypeptide in a
sample derived from a subject.
"Detection" - refers to a method of detection of a disease. This term may refer to detection of a
predisposition to a disease, or to the detection of the severity of the disease.
By "homolog/homology", as utilized in the present invention, is meant at least about 70%,
preferably at least about 75% homology, advantageously at least about 80% homology, more
advantageously at least about 90% homology, even more advantageously at least about 95%,
e.g., at least about 97%, about 98%, about 99% or even about 100% homology. The invention
also comprehends that these polynucleotides and polypeptides can be used in the same fashion
as the herein or aforementioned polynucleotides and polypeptides.
Alternatively or additionally, "homology", with respect to sequences, can refer to the number of
positions with identical nucleotides or amino acid residues, divided by the number of
nucleotides or amino acid residues in the shorter of the two sequences, wherein alignment of the
two sequences can be determined in accordance with the Wilbur and Lipman algorithm ((1983)
Proc. Natl. Acad. Sci. USA 80:726); for instance, using a window size of 20 nucleotides, a word
length of 4 nucleotides, and a gap penalty of 4, computer-assisted analysis and interpretation of
the sequence data, including alignment, can be conveniently performed using commercially
available programs (e.g., Intelligenetics™ Suite, Intelligenetics Inc., CA). When RNA
sequences are said to be similar, or to have a degree of sequence identity or homology with
DNA sequences, thymidine (T) in the DNA sequence is considered equal to uracil (U) in the
RNA sequence. RNA sequences within the scope of the invention can be derived from DNA
sequences or their complements, by substituting thymidine (T) in the DNA sequence with uracil
(U).
Additionally or alternatively, amino acid sequence similarity or homology can be determined,
for instance, using the BlastP program (Altschul et al., Nucl. Acids Res. 25:3389-3402) and
available at NCBI. The following references provide algorithms for comparing the relative
identity or homology of amino acid residues of two polypeptides, and additionally, or
alternatively, with respect to the foregoing, the teachings in these references can be used for
determining percent homology: Smith et al,, (1981) Adv. Appl. Math. 2:482-489; Smith et al.,
(1983) Nucl. Acids Res. 11:2205-2220; Devereux et al., (1984) Nucl. Acids Res. 12:387-395;
Feng et al., (1987) J. Molec. Evol. 25:351-360; Higgins et al., (1989) CABIOS 5:151-153; and
Thompson etal., (1994) Nucl. Acids Res. 22:4673-4680.
"Having at least X% homolgy" - with respect to two amino acid or nucleotide sequences, refers
to the percentage of residues that are identical in the two sequences when the sequences are
optimally aligned. Thus, 90% amino acid sequence identity means that 90% of the amino acids
in two or more optimally aligned polypeptide sequences are identical.
An additional embodiment of the present invention concerns a pharmaceutical composition
comprising an RTP801 inhibitor in a therapeutical ly affective amount as an active ingredient
and a pharmaceutically acceptable carrier. The inhibitor may be a biological inhibitor, an
organic molecule, a chemical molecule, etc. said pharmaceutical composition may comprise an
RTP801 inhibitor which is a polynucleotide which comprises consecutive nucleotides having a
sequence which is an antisense sequence to the sequence set forth in Figure 1 (SEQ ID No: 1).
Further, the RTP801 inhibitor may be a vector comprising these polynucleotides. Additionally,
the RTP801 inhibitor may be a monoclonal antibody which specifically binds to an epitope
comprising 4-25 amino acids set forth in Figure 2 (SEQ ID No:2), or an RNA molecule which
targets the RTP801 gene mRNA such as an siRNA molecule (optionally depicted in Tables A-C
and in particular, siRNA Nos: 22,23,25,27, 39,41, 42, 49 and 50 of Table A) or a ribozyme.
The active ingredients of the pharmaceutical composition can include oligonucleotides that are
nuclease resistant needed for the practice of the invention or a fragment thereof shown to have
the same effect targeted against the appropriate sequence(s) and/or ribozymes. Combinations of
active ingredients as disclosed in the present invention can be used, including combinations of
antisense sequences.
An additional embodiment of the present invention provides for the use of a therapeutically
effective dose of an RTP801 inhibitor for the preparation of a medicament for promoting
recovery in a patient suffering from spinal cord disease or injury. In one embodiment the
inhibitor is preferably an siRNA. In another embodiment the inhibitor is preferably Structure A
depicted herein.
The invention has been described in an illustrative manner, and it is to be understood that the
terminology which has been used is intended to be in the nature of words of description rather than
of limitation.
Obviously, many modifications and variations of the present invention are possible in light of the
above teachings. It is, therefore, to be understood that within the scope of the appended claims, the
invention can be practiced otherwise than as specifically described.
Throughout this application, various publications, including United States patents, are referenced
by author and year and patents by number. The disclosures of these publications and patents and
patent applications in their entireties are hereby incorporated by reference into this application in
order to more fully describe the state of the art to which this invention pertains.
BRIEF DESCRIPTION OF THE FIGURES
Fig. 1 details the coding sequence of the RTP801 gene (SEQ ID NO: 1);
Fig. 2 details the amino acid sequence of the RTP801 polypeptide (SEQ ID NO:2);
100
Fig. 3 is a diagram depicting the exons, CDS, human SNPs and the position of the
various nucleic acid molecules which are either human specific or specific for
human, mouse and rat in parallel;
Fig. 4A-H depict a panel of Western Blot analysis results obtained upon applying various
double-stranded nucleic acids according to the present invention to a first human
cell line, whereby the experiment was carried out twice, referred to as experiment
1 and experiment 2, and whereby the expression level of pllOa and p85 is
represented as loading controls and the intensity (density) of the RTP801 band is
a measure for the inhibitory activity of the particular double-stranded nucleic acid
applied;
Fig. 5A-F depict a panel of Western Blot analysis results obtained upon applying various
double-stranded nucleic acids according to the present invention to a second
human cell line, whereby the experiment was carried out twice, referred to as
experiment 1 and experiment 2, and whereby the expression level of pllOa and
p85 is represented as loading controls and the density of the RTP801 band is a
measure for the inhibitory activity of the particular double-stranded nucleic acid
applied;
Fig. 6A-C depict a panel of Western Blot analysis results obtained upon applying various
double-stranded nucleic acids according to the present invention to the first
human cell line at different concentrations, namely 10 nM (5A), 5 nM (5B) and 1
nM (5C), whereby the experiment was carried out twice, referred to as
experiment 1 and experiment 2, and whereby the expression level of pllOa and
p85 is represented as loading controls and the density of the RTP801 band is a
measure for the inhibitory activity of the particular double-stranded nucleic acid
applied;
Fig. 7 depicts a panel of Western Blot analysis results obtained applying various
double-stranded nucleic acids according to the present invention to a mouse cell
line, whereby the experiment was carried out twice, referred to as experiment 1
and experiment 2, and whereby the expression level of pllOa and p85 is
represented as loading controls and the density of the RTP801 band is a measure
for the inhibitory activity of the particular double-stranded nucleic acid applied;
Fig. 8 shows the results of experiments in a mouse AMD model system;
Fig. 9 shows the results of additional experiments in a mouse AMD model system;
Fig. 10 shows the results of experiments in a non-human primate AMD model system;
Fig. 11A-B shows the results of additional experiments in a non-human primate AMD model
system;
Fig. 12A-B shows the results of further additional experiments in a non-human primate AMD
model system;
Fig. 13A-B represents an analysis of the experimental results achieved in a non-human
primate AMD model;
Fig. 14 represents an additional analysis of the experimental results achieved in a nonhuman
primate AMD model.
Fig. 15 A-C shows the results of an experiment involving the intratracheal instillation of an
RTP801 expressing plasmid into mice;
Fig. 16 A-C shows the results of a short-term (7 days) cigarette smoking model in RTP801
KO and WT mice;
Fig. 17 A-C shows the results of a short-term cigarette smoking model in WT mice instilled
with active anti-RTP801 (REDD 14) and control (REDDS) siRNA.
Fig 18 shows the results of experiments with RTP801 KO mice in a long-term CS
model;
Fig. 19 shows the results of experiments in a mouse ARF model system;
Fig. 20 shows the results of experiments in a mouse Diabetic Retinopathy model system;
Fig. 21 shows the results of additional experiments in a mouse Diabetic Retinopathy
model system;
Fig. 22 shows the results of further additional experiments in a mouse Diabetic
Retinopathy model system;
Fig. 23 shows the results of combined RTP801 / VEGF inhibition experiments in a
mouse CNV model system;
Fig. 24 shows the results of additional combined RTP801 / VEGF inhibition experiments
in a mouse CNV model system;
Fig. 25 shows the results of experiments studying effect of RTP801 siRNA on gene
expression in RPE and neural retina;
Fig. 26 A-B shows additional results of experiments studying effect of RTP801 siRNA on
gene expression in RPE and neural retina; and
Fig. 27 shows the results of experiments demonstrating that RT801NP is as active as
RTP801.
EXAMPLES
Without further elaboration, it is believed that one skilled in the art can, using the preceding
description, utilize the present invention to its fullest extent. The following preferred specific
embodiments are, therefore, to be construed as merely illustrative, and not limitative of the
claimed invention in any way.
Standard molecular biology protocols known in the art not specifically described herein are
generally followed essentially as in Sambrook et al., Molecular cloning: A laboratory manual,
Cold Springs Harbor Laboratory, New-York (1989, 1992), and in Ausubel et al., Current
Protocols in Molecular Biology, John Wiley and Sons, Baltimore, Maryland (1988).
Standard organic synthesis protocols known in the art not specifically described herein are
generally followed essentially as in Organic syntheses: Vol.1- 79, editors vary, J. Wiley, New
York, (1941 - 2003); Gewert et al., Organic synthesis workbook, Wiley-VCH, Weinheim
(2000); Smith & March, Advanced Organic Chemistry, Wiley-Interscience; 5th edition (2001).
Standard medicinal chemistry methods known in the art not specifically described herein are
generally followed essentially as in the series "Comprehensive Medicinal Chemistry", by
various authors and editors, published by Pergamon Press.
The features of the present invention disclosed in the specification, the claims and/or the
drawings may both separately and in any combination thereof be material for realizing the
invention in various forms thereof.
Example 1
General Materials and methods
If not indicated to the contrary, the following materials and methods were used in Examples 1-5:
Cell culture
The first human cell line, namely HeLa cells (American Type Culture Collection) were cultured
as follows: Hela cells (American Type Culture Collection) were cultured as described in
Czauderna F et al. (Czauderna, F., Fechtner, M., Aygun, H., Arnold, W., Klippel, A., Giese, K.
& Kaufmann, J. (2003). Nucleic Acids Res, 31, 670-82).
The second human cell line was a human keratinozyte cell line which was cultivated as follows:
Human keratinocytes were cultured at 37 °C in Dulbecco's modified Eagle medium (DMEM)
containing 10% FCS.
The mouse cell line was B16V (American Type Culture Collection) cultured at 37 °C in
Dulbecco's modified Eagle medium (DMEM) containing 10% FCS. Culture conditions were as
described in Methods Find Exp Clin Pharmacol. 1997 May; 19(4):231-9:
In each case, the cells were subject to the experiments as described herein at a density of about
50,000 cells per well and the double-stranded nucleic acid according to the present invention
was added at 20 nM, whereby the double-stranded nucleic acid was complexed using 1 ng/ml of
a proprietary lipid.
Induction ofhypoxia-like condition
The cells were treated with CoCb for inducing a hypoxia-like condition as follows: siRNA
transfections were carried out in 10-cm plates (30-50% confluency) as described by (Czauderna
et al., 2003; Kretschmer et al., 2003). Briefly, siRNA were transfected by adding a preformed
1 Ox concentrated complex of GB and lipid in serum-free medium to cells in complete medium.
The total transfection volume was 10 ml. The final lipid concentration was 1.0 ug/ml; the final
siRNA concentration was 20 nM unless otherwise stated. Induction of the hypoxic responses
was carried out by adding CoCh (lOOuM) directly to the tissue culture medium 24 h before
lysis.
Preparation of cell extracts and immuno blotting
The preparation of cell extracts and immuno blot analysis were carried out essentially as
described by Klippel et al. (Klippel, A., Escobedo, M.A., Wachowicz, M.S., Apell, G., Brown,
T.W., Giedlin, M.A., Kavanaugh, W.M. & Williams, L.T. (1998). Mol Cell Biol, 18, 5699-711;
Klippel, A., Reinhard, C., Kavanaugh, W.M., Apell, G., Escobedo, M.A. & Williams, L.T.
(1996). Mol Cell Biol, 16, 4117-27). Polyclonal antibodies against full length RTP801 were
generated by immunising rabbits with recombinant RTP801 protein producing bacteria from
pET19-b expression vector (Merck Biosciences GmbH, Schwalbach, Germany). The murine
monoclonal anti-pi lOa and anti-p85 antibodies have been described by Klippel et aJ. (supra).
Example 2
Reduction of RTP801 expression in a first human cell line
Various double-stranded nucleic acids were prepared. Their location relative to the mRNA and
CDS as well as human SNPs in the nucleic acid coding for human RTP801 (databank accession
no. NM_019058) is depicted in Figure 3. The first human cell line was contacted with said
double-stranded nucleic acids as described in example 1. Upon induction of a hypoxia-like
condition and treatment with said double-stranded nucleic acids the cells were lysed and the cell
lysates subjected to immunoblotting. pi lOa, which is a catalytic unit of the PI3-kinase, and p85
were used as loading controls. The intensity of the RTP801 band as visualised using the
RTP801 polyclonal antibodies is a measure of the activity of the individual double-stranded
nucleic acids in terms of reducing the expression level of RTP801.
Each and any of the double-stranded nucleic acids has been such modified such that a 2' O-Me
group was present on the first, third, fifth, seventh, ninth, eleventh, thirteenth, fifteenth,
seventeenth and nineteenth nucleotide of the antisense strand, whereby the very same
modification, i. e. a 2'-O-Me group was present at the second, fourth, sixth, eighth, tenth,
twelfth, fourteenth, sixteenth and eighteenth nucleotide of the sense strand. Additionally, it is to
be noted that in case of these particular nucleic acids according to the present invention the first
stretch is identical to the first strand and the second stretch is identical to the second strand and
these nucleic acids are also blunt ended.
The experiments were performed twice and the individual results shown in Figs. 4A to H, where
they are designated as experiment 1 and experiment 2, respectively.
The representations h, hr and hmr in Figs. 4A to H indicate that the respective double-stranded
nucleic acid was designed such as to address a section of the RTP801 mRNA which is specific
for human RTP801 mRNA (h), to address a section of the RTP801 mRNA which is specific for
human and rat RTP801 mRNA (hr) and to address a section of the RTP801 mRNA which is
specific for human, mouse and rat RTP801 mRNA (hmr). The double-stranded nucleic acid
referred to as no. 40.1 was used as a positive control and untreated cells (UT+) were used as
negative control.
In accordance with the results, the following double-stranded nucleic acids turned out to be
particularly useful in down-regulating the expression of RTP801: no. 14, no. 15, no. 20, no. 21,
no. 22, no. 23, no. 24, no. 25, no. 27, no. 39, no. 40, no. 41, no. 42, no. 43, no. 44, no. 49 and no.
50 (see Table A).
Example3
Reduction of RTP801 expression in a second human cell line
The experiments as described in connection with Example 2 were repeated using the second
human cell line as specified in Example 1 and the results are depicted in Figs. 5A to F.
As may be deduced from these figures, the results as obtained in connection with the
experiments described in Example 2, were confirmed using this second human cell line.
Example 4
Dosage effect of RTP801-specific double-stranded nucleic acids
In this experiment, the dosage effect of RTP801-specific double-stranded nucleic acids was
investigated.
For that purpose, the HeLa cells treated as in connection with Examples 2 and 3, whereby the
concentration of double-stranded nucleic acid in the cultivation broth was 10 nM, 5 nM and 1
nM. As positive control, double-stranded nucleic acid no. 40.1 was used, as negative control
untreated cells (UT+). The read out was the same as described in connection with Examples 2
and 3. The particular double-stranded nucleic acids used were those with internal reference
numbers 14, 22, 23 and 27 which are directed to stretches on the RTP801 mRNA which are
shared by humans, mice and rats, and double-stranded nucleic acid with internal reference
numbers 39 and 42 which are directed to stretches of the RTP801 mRNA specific for human
RTP801.
The results are shown in Fig. 6A to C. From said figures it can be taken that there is a clear
concentration dependency of the effect of the double-stranded nucleic acids specific for
RTP801, whereby the nucleic acid molecules having internal reference numbers 1, 15, 20, 21,
24, 40,41, 43, 44,, 22, 23, 27, 39, 42,40.1, 44.1, and 14, preferably 22,23,27, 39, 42,40.1 and
44.1 and more preferably 14, 23 and 27 and preferably each of said nucleic acid molecule
having the particular modification pattern as described for them in the example part herein are
particularly effective
Example 5
Species specificity of the RTP801-specific double-stranded nucleic acid
The double-stranded nucleic acids according to the present invention have been designed against
stretches of the RTP801 mRNA which are the same or different in various species. To test
whether there is a species specificity of a RTP801-specific double-stranded nucleic acid, the
double-stranded nucleic acids with internal reference numbers 14, 22, 23 and 27 which address a
stretch of the RTP801 mRNA which is conserved among human, mouse and rat RTP801
mRNA, and the double-stranded nucleic acids with internal reference numbers 39 and 42 which
address a stretch of the RTP801 mRNA which is specific for human RTP801 mRNA, i. e. which
addresses a stretch which as such is not present in mouse or rat, were compared in terms of
down-regulating RTP801 using the same approach and read-out as specified in Examples 1 and
2.
Although all of the double-stranded nucleic acids used are in principle active against human
mRNA and, as shown in the preceding examples, are also suitable to down-regulate the
expression of RTP801, upon using a mouse cell line only those double-stranded nucleic acids
which are also specific for mouse RTP801 mRNA effectively reduced RTP801 expression,
namely double-stranded nucleic acids nos. 14, 22,23 and 27.
From this result it can be concluded that it is possible to design RTP801 addressing doublestranded
nucleic acids which are specific for one or several species. This allows use of the very
same molecule in animal models as well as in man.
Example 6
Experimental models, methods and results relating to Macular Degeneration
The compounds of the present invention were tested in the following an animal model of
Choroidal neovascularization (CNV). This hallmark of wet AMD is induced in model animals
by laser treatment.
A) MOUSE MODEL
Choroidal neovascularization (CNV) induction
Choroid neovascularization (CNV), a hallmark of wet AMD, was triggered by laser
photocoagulation (532 nm, 200 mW, 100 ms, 75 urn) (OcuLight GL, Index, Mountain View,
CA) performed on both eyes of each mouse on day 0 by a single individual masked to drug
group assignment. Laser spots were applied in a standardized fashion around the optic nerve,
using a slit lamp delivery system and a cover slip as a contact lens.
Treatment groups
CNV was induced in the following groups of mice (males 6-8 weeks of age):
(l)12WTmice;
(2) 12 RTP801 Knock-Out mice;
(3) 12 WT mice injected with 0.25 fig of synthetic stabilized active anti-RTP801
siRNA (REDD 14) in one eye and inactive anti-RTP801 siRNA (REDD8 -
negative control) in the fellow eye, at days 0 and 7;
(4) 12 WT mice injected with 0.25 \ig of synthetic stabilized active anti-RTP801
siRNA (REDD 14) in one eye and inactive anti-GFP siRNA (negative control) in
the fellow eye at days 0 and 7;
(5) 12 WT mice injected with either 0.1 ug of synthetic stabilized active anti-
RTP801 siRNA (REDD 14) in one eye and PBS (negative control) in the fellow
eye at days 0 and 7;
(6) 12 WT mice injected with either 0.05 ug of synthetic stabilized active anti-RTP801
siRNA (REDD14) in one eye and PBS (negative control) in the fellow eye at days 0 and
7.
Both eyes of each mouse were laser-treated. The volume injected was 2 \i\.
Evaluation
1. The experiment was terminated at day 14. For evaluation, the eyes were enucleated and
fixed with 4% paraformaldehyde for 30 min at 4°C. The neurosensory retina was
detached and severed from the optic nerve. The remaining RPE-choroid-sclera complex
was flat mounted in Immu-Mount (Vectashield Mounting Medium, Vector) and
coverslipped. Flat mounts were examined with a scanning laser confocal microscope
(TCS SP, Leica, Germany). Vessels were visualized by exciting with blue argon laser.
Horizontal optical sections (1 urn step) were obtained from the surface of the RPEchoroid-
sclera complex. The deepest focal plane in which the surrounding choroidal
vascular network connecting to the lesion could be identified was judged to be the floor
of the lesion. Any vessel in the laser treated area and superficial to this reference plane
was judged as CNV. Images of each section were digitally stored. The area of CNVrelated
fluorescence was measured by computerized image analysis using the Leica TCS
SP software. The summation of whole fluorescent area in each horizontal section was
used as an index for the volume of CNV.
2. Separate WT mice (5 eyes per group) were used for evaluating RTP801 mRNA
expression in CNV (as well as the expression of other genes relevant to AMD)
(untreated and treated with siRNA) using real-time PCR on RNA extracted from
RPE/choroids, or from neural retina.
Results
1. RTP801 KO mice displayed 30% less blood vessel leakage compared to WT mice
following CNV induction; see Figure 8.
2. Synthetic stabilized siRNA against RTP801, REDD14, elicited a dose-dependent
reduction of the CNV volume. A maximum of -70% inhibition compared to PBSinjected
eyes was achieved at a REDD 14 (sequence No. 14 in table 1, SEQ ID No.s 16
(sense) and 66 (antisense)) dose of 0.25 ug per eye. At the same dose, both negative
control siRNAs, REDD8 and anti-GFP siRNA, displayed only 27% and 33% CNV
volume reduction respectively, supporting both the superior efficacy of REDD 14 and
also the specificity of its effect.
B) NON-HUMAN PRIMATE MODEL
CNV induction
Eight male cynomoglus monkeys (Macaco fascicularis) 2-6 years of age were used for the
study. Choroidal neovascularization (CNV) was induced by perimacular laser treatment of both
eyes prior to doseadministration. Nine lesions were placed in the macula with a laser [OcuLight
GL (532 nrn) Laser Photo-coagulator with an IRIS Medical® Portable Slit Lamp Adaptor], and
laser spots in the right eye were mirror the placement in the left eye. The approximate laser
parameters were as follows: spot size: 50-100 urn diameter; laser power: 300-700 milliwatts;
exposure time: 0.1 seconds.
Treatment
Immediately following laser treatment, both eyes of all animals were subjected to a single
intravitreal injection. Left eye was dosed with 350 ug of synthetic stabilized siRNA against
RTP801 (the same one used in the mouse study) in the final volume of 50 ul, whereas the
contralateral eye received 50 ul of PBS (vehicle).
Evaluation
1. All the animals were subjected to daily examination of food consumption and body
weight measurements.
2. 2 monkeys were euthanized at day 6 following CNV induction. Their eyes were
enucleated and posterior pole was flattened. Then the fovea region was excised and
separated into choroids and neuroretina which were separately (for every animal) frozen
in liquid nitrogen to be subsequentlyused for UNA extraction and real time PCR
evaluation of RTP801 expression.
3. Fluorescein angiograms were performed pre-study, and at the end of weeks 1, 2, and 3
following CNV induction. Photographs were taken, using a fundus camera (TRC-50EX
Retina Camera). Images were captured using the TOPCON IMAGEnet™ system.
Fluorescein dye (10% fluorescein sodium, approximately 0.1 mL/kg) was injected via
vascular access ports. Photographs were taken at several timepoints following dye
injection, to include the arterial phase, early arteriovenous phase and several late
arteriovenous phases in order to evaluate neovascularization snd to monitor leakage of
fluorescein associated with CNV lesions. Interpretation and analysis of the fluorescein
angiograms was independently conducted by two ophthalmologists.
Neovascularization (NV) was assessed in early angiograms and every spot was graded
according to the following scheme:
0 - no signs of NV
0.5 - suspicious spot
1 - "hot" spot
2 - NV in the laser burn
112
3 - evident NV
Leakage was assessed according to the following scheme:
0 - no leakage
0.5 - suspicious spot
1 - evident small spot leakage
2 - leakage growing with time
3 ~ leakage greater than previous borders (evidently)
In addition, the size of every spot was compared between the early and the late angiograms
using morphometric measurements, and the increase in the spot's size resulting from the leakage
was calculated.
4. Electroretinograms (ERGs) were recorded using an Epic 2000 electroretinograph
according to Sierra's SOPs and the study-specific SOP, including the use of the
Ganzfield apparatus, at prestudy and in the end of week 3 The tabulated ERG data were
evaluated by a veterinary ophthalmologist.
The study was terminated at day 21 post CNV induction. Gross necropsy and histological
examination were performed on organs and tissues including the eyes.
Results
1. siRNA against RTP801 reduced RTP801 expression in the'RPE/choroids of laser-treated
animals, as measured at day 6 post CNV induction by real-time PCR (see Figure 10).
2. Comparison of the spot grading for leakage and neovascularization between the fellow eyes
in each individual monkey revealed that both of these pathological characteristics were
diminished in the eyes injected with RTP801 siRNA as compared to the control (for leakage
results, see Figure 11; for neovascularization results, see Figure 12).
3. Calculation of the overall number of spots with higher clinically-relevant grades (2 and 3) of
leakage or neovascularization in all siRNA-injected eyes compared to all PBS-injected eyes
again revealed that siRNA injected eyes were less affected (see Figure 13, a+b).
4, The overall grading data for leakage of spots and neovascularisation was subjected to
statistical evaluation. The existence of differences between the siRNA and control treatments
was analyzed by calculating the delta between the mean spot ranks of the control right (R)
eye and siRNA-injected left (L) eye (delta=R-L). The significance of the difference was
calculated using a non-parametric statistical method, Wilcoxon signed ranks test - a one tail
test. Different phases of angiograms (early arterial, arterio-venous and late venous) were
analyzed separately for every week (1,2, and 3).
Table 1 shows the significance (one tail test) of leakage rank difference from 0 for each
group (p-values left eyes (siRNA treated) with respect to the right (Placebo treated) in week 2 and 3 in the
late angiograms.
TABLE 1
(Table Removed)
Note that late angiograms are usually utilized for evaluation of leakage parameters.
Table 2 shows the significance (one tail test) of neovascularization (NV) rank difference
from 0 for each group (p-values TABLE 2
(Table Removed)
A significant NV rank reduction was found in the left eyes with respect to the right in week 2
and 3 in the early period and in the Arterio Venus period in week 2.
Note that early angiograms are usually utilized for evaluation of neovascularization parameters.
5. Quantitative morphornetric evaluation of the increase in area of the spots occurring between
early (arterial phase) and late (venous phase) angiograms due to the leakage revealed that
this parameter was significantly reduced in the laser spots within siRNA-injected eyes (left
eyes, OS) compared to control (right eyes, OD). Two examples are shown in Figure 14. The
graphs demonstrate the relative increase (in %) in the area of every spot in the left and right
eye of animals #3315 and 3300.
Additionally, it was noted throughout all the above studies that anti RTP-801 siRNA had no
adverse effects on electroretinograms (ERG), on eye histology or on structure and function of
other organs and systems.
To summarize the above experiments and results:
1. Both genetic (RTP801 -/-) and therapeutic siRNA inhibition of RTP801 expression in the
laser-induced CNV model of wet age-related macular degeneration (wet AMD) result in
significant reduction of the CNV volume.
2. Positive results were obtained in mouse and non-human primate model.
3. Pathological and ERG examination in monkey did not reveal any siRNA-mediated
toxicity either in eyes or in any other organs or systems.
C) EFFICACY OF COMBINATION THERAPY OF RTP801 SIRNA (REDD 14) AND ANTIVEGF
ANTIBODY
The efficacy of combination therapy of RTP801 siRNA (REDD14) and anti-VEGF antibody in
the treatment of diseases in which CNV occurs was tested in the above mouse CNV model.
A) CNV volume studies
The volume of choroidal neovascularization (CNV) 3 weeks after laser injury was computed
byconfocal fluorescence microscopy as previously described (Sakurai et al. IOVS 2003;44:
3578-85 & Sakurai et al. IOVS 2003; 44: 2743-2749).

In previous studies we found that anti-VEGF-A antibody (Ab) reduced CNV volume in a dose
dependent fashion. A dose of 1 ng of VEGF-A Ab was chosen for the REDD14+VEGF-A Ab
combination studies because this dose had an intermediate inhibitory effect: VEGF-A Ab (1 ng)
reduced the size of CNV by 26±6%.
The principal findings of the REDD 14 + VEGF-A antibody (Ab) study are:
• The addition of REDD 14 at the lower 0.05 ng dose reduced the size of CNV by 27±4%
compared to VEGF-A Ab alone.
• The addition of REDD14 at the higher 0.25 ug dose reduced the size of CNV by 55±3%
compared to VEGF-A Ab alone.
B) CNV leakage studies
Experiment 1
This experiment was designed in order to identify a potential additive or synergistic therapeutic
effect of inhibition of VEGF and RTP801 in the model of laser-induced choroid
neovascularization in mice
Materials:
• REDD 14 (RTP801 siRNA)
• REDD8 (negative control)
• Anti-VEGF antibodies
• Non-specific IgG (negative control)
CNV was induced on day zero as described above; the test material was injected to the subjects
on day zero and day 7.
The results were evaluated by Fluorescein angiography on weeks 1,2, 3, and by CNV volume
measurement on week 3. each test group was composed of 10 eyes.
Experimental groups:
• VEGF Ab 0.5 ng/eye
• VEGF Ab 1 ng/eye
• VEGF Ab 2 ng/ eye
• VEGF Ab 4 ng/eye
• REDD 14 0.05 ug/eye
• REDD 14 0.1 ug/eye
• REDD 14 0.25 ug/eye
• REDD 14 0.05 ug/eye + VEGF Ab 1 ng/eye
• REDD 140.1 ug/eye + VEGF Ab 1 ng/eye
• REDD 14 0.25 ug/eye + VEGF Ab I ng/eye
Control groups
• PBS
• Non-specific IgG 2 ng/eye
• REDDS 0.1 ug/eye
• REDDS 0.1 ug/eye + VEGF Ab 1 ng/eye
Results
The results of the above experiment are presented in Figures 23-24. These results show that
simultaneous intravitreal administration of VEGF Ab and REDD 14 leads to augmented and
dose-dependent inhibition of Choroid neovascularization and Choroid blood vessel leakage, as
expressed in reduced incidence of Grade 4 spots and increased incidence of Grade 1 spots.
Angiograms were graded using a modification of a semi-quantitative grading (1-4) scheme
previously published (Sakurai et al. IOVS 2003; 44: 2743-2749). Grade 1 lesions are considered
as never having formed, i.e., equivalent to complete prevention. Grade 4 lesions are considered
pathologically significant, i.e., equivalent to lesions that would be treated in patients.VEGF-A
Ab (1 ng) reduced the incidence of Grade 4 lesions per eye by 38±8% and increased the
incidence of Grade 1 lesions per eye by 66±43%.
The principal findings of the REDD 14 + VEGF-A Ab combination leakage study are:
• The addition of REDD 14 at the lower 0.05 ug dose reduced the incidence of Grade 4 lesions
by 66±12% compared to VEGF-A Ab alone.
• The addition of REDD 14 at the higher 0.25 ng dose reduced the incidence of Grade 4 lesions
by 60± 12% compared to VEGF-A Ab alone.
• The addition of REDD 14 at the higher 0.25 jig dose doubled (100±34%) the incidence of
Grade 1 lesions compared to VEGF-A Ab alone.
118
Experiment 2
This experiment was designed in order to study the effect of REDD 14 on gene expression in
RPE and neural retina.
Experimental design
Groups:
• PBS
• REDD 14 0.25 mg
The Group size was 5 eyes. CNV was induced by laser treatment as described above on day
zero; the test material was also injected on day zero, and the effect evaluated by qPCR analysis
of gene expression in RPE and neural retina on days zero and 5.
Results
The results of the above experiment are presented in Figure 25. These results show that the
administration of REDD 14 causes:
• -40% downregulation of RTP801 expression below the baseline both in RPE and
in neural retina (see also Figure 26);
• ~ 70% upregulation of PEDF expression over the baseline in neural retina (note:
in PBS-injected eyes expression of PEDF is 40% downregulated below the
baseline)
• -40% downregulation of VEGF164 expression below the baseline in RPE (note:
in PBS-injected eyes, expression of VEGF164 is 20% downregulated)
• -50% reduction of MCP1 expression in RPE/choroids (Figure 26)
General conclusions from both experiments:
• Simultaneous inhibition of RTP801 and VEGF has enhanced inhibitory effect on
choroid neovascularization and neovascular leakage.
• Inhibition of RTP801 expression by REDD 14 not only prevents PEDF
downregulation in the CNV model but enhances its expression compared to the
baseline.
• Inhibition of RTP801 expression leads to concomitant downregulation of MCP1
which should have an anti-inflammatory effect.
• Without being bound by theory, the increase of PEDF expression by REDD 14 may
underlie the observed cooperative effect of simultaneous inhibition of VEGF and
RTP801
(Note: PEDF is a well-known antiangiogenic and neuroprotective factor.)
• Without being bound by theory, the reduction of MCP1 expression by REDD14
may also underlie the observed cooperative effect of simultaneous inhibition of
VEGF and RTP801
(Note: MCP1 is a known pro-inflammatory chemokine involved in pathogenesis of AMD.)
Additional AMD models which may be used to test the methods of the present invention:
• Ccl-2 or Ccr-2 deficient animals - deficiency in either of these proteins causes
the development of some of the main features of AMD. Animals deficient in
these proteins can be used to test the methods of the present invention.
For further information on AMD animal models, see: Chader, Vision research 42 (2002) 393-
399; Ambati et al., Nature Medicine 9(11) (2003) 1390-1397; Tolentino et al., Retina 24 (2004)
132-138.
D) Comparison of activity of REDD 14 anti RTP801 siRNA possessing a 3'phosphate group
on each strand with the same molecule lacking 3' phosphates (REDD14NP) in the laserinduced
CNV model.
The experiment was generally performed and evaluated as described above. One eye of each
mouse (12 per group) was injected with 0.25 ug of REDD 14 siRNA whereas another eye was
injected with REDD MNP siRNA.
Results
Both siRNAs equally efficiently reduced CNV volume (Fig. 27).
Example 7
Models and results relating to COPD and Emphysema
The compounds of the present invention were tested in the following an animal models:
* Cigarette smoke-induced emphysema model: chronic exposure to cigarette smoke causes
emphysema in several animals such as, inter alia, mouse, guinea pig.
* Lung protease activity as a trigger of emphysema.
* VEGFR inhibition model of emphysema.
* Bronchial instillation with human neutrophil / pancreatic elastase in rodents.
* MMP (matrix metalloprotease)-induced enphysema.
* Inflammation-induced emphysema.
Additionally, emphysema models may be generated through genetic means (e.g., mice carrying
the TSK mutation), and emphysematous animals may be generated by known modifiers of
susceptibility to emphysema such as, inter alia, lung injury, alveolar hypoplasia, hyperoxia,
glucocorticoid treatment and nutrition.
A. Evaluation of the influence of lack of RTP801 on disease development in mouse
models of emphysema (using RTP801 knockout mice)
(1) Cigarette smoking (CS) induced inflammation and apoptosis is initiated in 5 RTP801
KO and 5 control wild type 4 months old male mice. The mice are subjected to intense
CS (as described in Rangasamy et al., see above) for 7 days. KO and WT non-treated
mice from the VEGFR inhibition experiment above can also serve as non-treated control
groups for this experiment. The lungs are subsequently agarose-inflated, fixed and
imbedded in paraffin, and development oxidative stress in the KO mice is assessed by:
a) immunohistochemical localization and quantitation of 8-oxb-dG in the
lung sections;
b) immunohistochemical localization and quantitation of active caspase 3 in
the lung sections using specific antibodies, or quantitative evaluation of
the number of TUNEL-positive cells;
c) measurement of ceramide concentration in the lung extracts;
d) measurement of caspase activity in the lung extracts.
(2) Long-term cigarette smoking in the KO mice.
6 KO and 6 age-matched WT female mice were subjected to intense cigarette smoking (5 hrs a
day) during a period of 6 months. The mice were then sacrificed, and average interseptal
diameter (a parameter of emphysema development) was evaluated using a morphometric
approach.
B. Evaluation of the influence of lack of RTP801 on disease progression in mouse
models of emphysema by inhibiting endogenous RTP801 employing intralung delivery
RTP801 -inactivating siRNA
CS-induced inflammation was induced by 7 day smoking in 2 groups of C57BL6 mice, 10
mice per group. Group 1: CS + delivery of control siRNA (REDDS) siRNA; Group 2: CS +
RTP801 siRNA (REDD 14). Control groups of mice were instilled with either type of siRNA but
kept in room air conditions. The animals were evaluated as in the above experiment with the
Knock-Out mice.
Methods
Exposure to cigarette smoking (CS)
Exposure is carried out (7 h/day, 7 days/week) by burning 2R4F reference cigarettes (2.45 mg
nicotine per cigarette; purchased from the Tobacco Research Institute, University of Kentucky,
Lexington, KY, USA) using a smoking machine (Model TE-10, Teague Enterprises, Davis, CA,
USA). Each smoldering cigarette was puffed for 2 s, once every minute for a total of eight puffs,
at a flow rate of 1.05 L/min, to provide a standard puff of 35 cm3. The smoke machine is
adjusted to produce a mixture of sidestream smoke (89%) and mainstream smoke (11%) by
burning five cigarettes at one time. Chamber atmosphere is monitored for total suspended
particulates and carbon monoxide, with concentrations of 90 mg/m3 and 350 ppm, respectively.
Morphologic and morphometric analyses
After exposing the mice to CS or instillation of RTP801 expressing plasmid, the mice are
anesthetized with halothane and the lungs are inflated with 0.5% low-melting agarose at a
constant pressure of 25 cm as previously described6. The inflated lungs are fixed in 10%
buffered formalin and embedded in paraffin. Sections (5 urn) are stained with hematoxylin and
eosin. Mean alveolar diameter, alveolar length, and mean linear intercepts are determined by
computer-assisted morphometry with the Image Pro Plus software (Media Cybernetics, Silver
Spring, MD, USA). The lung sections in each group are coded and representative images (15 per
lung section) are acquired by an investigator masked to the identity of the slides, with a Nikon
E800 microscope, 20X lens.
Bronchoalveolar lavage (BAD and phenotyping
Following exposure to CS or instillation of RTP801 expressing plasmid, the mice are
anesthetized with sodium pentobarbital. The BAL fluid collected from the lungs of the mice is
centrifuged (500 'g at 4°C), and the cell pellet is resuspended in phosphate-buffered saline. The
total number of cells in the lavage fluid is determined, and 2 x 104 cells are cytocentrifuged
(Shandon Southern Products, Pittsburgh, PA, USA) onto glass slides and stained with Wright-
Giemsa stain. Differential cell counts are performed on 300 cells, according to standard
cytologic techniques .
Identification of alveolar apoptotic cell populations in the lungs.
To identify the different alveolar cell types undergoing apoptosis in the lungs, an
immunohistochemical staining of active caspase 3 is performed in the lung sections from the
room air (RA) as well as CS exposed mice. To identify the apoptotic type II epithelial cells in
the lungs, after active caspase 3 labeling, the lung sections are incubated first with anti-mouse
surfactant protein C (SpC) antibody and then with an anti-rabbit Texas red antibody. Apoptotic
endothelial cells are identified by incubating the sections first with the anti-mouse CD 31
antibody and then with the biotinylated rabbit anti-mouse secondary antibody. The lung sections
are rinsed in PBS and then incubated with the streptavidin-Texas red conjugated complex. The
apoptotic macrophages in the lungs are identified by incubating the sections first with the rat
anti-mouse Mac-3 antibody and then with the anti-rat Texas red antibody. Finally, DAPI is
applied to all lung sections, incubated for 5 minutes, washed and mounted with Vectashield
HardSet mounting medium. DAPI and fluorescein are visualized at 330-380 nm and 465-495
nm, respectively. Images of the lung sections are acquired with the Nikon E800 microscope,
40X lens.
Immunohistochcmical localization of active caspasc-3
Immunohistochemical staining of active caspase-3 assay is performed using anti-active caspase-
3 antibody and the active caspase-3-positive cells are counted with a macro, using Image Pro
Plus program. The counts are normalized by the sum of the alveolar profiles herein named as
alveolar length and expressed in urn. Alveolar length correlates inversely with mean linear
intercept, i.e., as the alveolar septa are destroyed, mean linear intercepts increases as total
alveolar length, i.e., total alveolar septal length decreases.
Caspase 3 activity assay
The caspase-3/7 activity is measured in lung tissue extracts using a fluorometric assay according
to the manufacturer's instructions. Snap-frozen lung tissue (n = 3 per group) was homogenized
with the assay buffer, followed by sonication and centrifugation at 800 x g. After removal of
nuclei and cellular debris, the supernatant (300 u.g protein) is then incubated with the profluorescent
substrate at room temperature for Ih and the fluorescence intensity was measured
utilizing a Typhoon phosphoimager (Amersham Biosciences, Inc., Piscataway, NJ, USA). The
results are expressed as the rate of specific caspase-3 substrate cleavage, expressed in units of
caspase 3 enzymatic activity, normalized by total protein concentration. Active recombinant
caspase 3 was utilized as the assay standard (0-4 U). Tissue lysates without substrate, assay
buffer alone, and lysates with caspase 3 inhibitor were utilized as negative controls.
Immunohistochemical localization of 8-oxo-dG
For the immunohistochemical localization and quantification of 8-oxo-dG, lung sections from
the mice exposed to CS or instilled with RTP801 expressing plasmid are incubated with anti-8-
oxo-dG antibody and stained using InnoGenexTM Iso-IHC DAB kit using mouse antibodies.
The 8-oxo-dG-positive cells are counted with a macro (using Image Pro Plus), and the counts
were normalized by alveolar length as described.
Instillation of plasmid DNA into mouse lungs
Plasmid DNA of RTP801 expressing and control vectors were prepared under endotoxin-free
DNA isolation kit. For intra-tracheal instillation, 50 ug of plasmid DNA is delivered in 80 ul
sterile perfluorocarbon. The oxygen carrying properties of perfluorocarbon make it well124
tolerated at these volumes, while its physical-chemical properties allow for extremely efficient
distal lung delivery when instilled intratracheally. Mice are anesthetized by brief inhalational
halothane exposure, the tongue is gently pulled forward by forceps and the trachea instilled with
perfluorocarbon solution applied at the base of the tongue via a blunt angiocatheter.
Instillation of siRNA into mouse lungs.
Mice are anesthetized with an intra-peritoneal injection of Ketamine/Xylazine (115/22 mg/kg).
50ug of siRNA is instilled intranasally in 50ul volume of 0.9% NaCl by delivering five
consecutive 10 uJ portions. At the end of the intranasal instillation, the mouse's head is held
straight up for 1 minute to ensure that all the instilled solution drains inside.
For further information, see: Rangasamy T, Cho CY, Thimmulappa, RK, Zhen L, Srisuma SS,
Kensler TW, Yamamoto M, Petrache I, Tuder RM, Biswal S. Genetic ablation ofNrft enhances
susceptibility to cigarette smoke-iduced emphysema in mice. Submitted to Journal ofdinincal
Investigation; Yasunori Kasahara, Rubin M. Tuder, Carlyne D. Cool, David A. Lynch, Sonia C.
Flores, and Norbert F. Voelkel. Endothelial Cell Death and Decreased Expression of Vascular
Endothelial Growth Factor and Vascular Endothelial Growth Factor Receptor 2 in
Emphysema. Am J Respir Crit Care Med Vol 163. pp 737-744, 2001; Yasunori Kasahara,
Rubin M. Tuder, Laimute Taraseviciene-Stewart, Timothy D. Le Cras, Steven Abman, Peter K.
Hirth, Johannes Waltenberger, and Norbert F. Voelkel. Inhibition of VEGF receptors causes
lung cell apoptosis and emphysema. J. Clin. Invest. 106:1311-1319 (2000); and a review on the
topic: Robin M. Tuder, Sharon McGrath and Enid Neptune, The pathological mechanisms of
emphysema models: what do they have in common?, Pulmonary Pharmacology & Therpaeutics
2002.
Results
1, Instillation of an RTP801 expressing plasmid results in an emphysema-like phenotype in
mouse lungs which is evident by (1) inctease in bronchoalveolar lavage cell counts (Fig.
125
15a); (2) apoptosis of lung septal cells (Figure 15b) and increase in the alveolar diameter
(Fig. 15c).
2. Instillation of RTP801 siRNA (REDD14) results in reduction of RTP801 expression in
the lungs (Fig. 17b).
3. RTP801 KO mice are protected from emphysema development following 6 months of
cigarette smoking as evident by the lack of enlargement of alveolar diameter. (Fig. 18 ).
4. RTP801 KO mice are protected from cigarette smoking induced inflammation as evident
by reduced number of inflammatory bronchoalveolage cells following 1 week of cigarette
smoking (Figure 16, a-b).
5. RTP801 KO mice are protected from cigarette smoking induced apoptosis of lung septal
cells as evidenced by lung section staining for activated caspase (Fig. 16c).
6. REDD14-instiIled mice are partially protected from cigarette smoking induced
inflammation as evident by reduced number of inflammatory bronchoalveolage cells
following 1 week of cigarette smoking (Figure 17a).
7. REDD 14-instilled mice are partially protected from cigarette smoking induced apoptosis
of lung septal cells as evidenced by lung section staining for activated caspase and by
immunoblotting of lung extracts with anti-activated caspase 3 antibodies ((Fig. 17c)
Example 8.
Models and results relating to microvascular disorders
The compounds of the present invention were tested in animal models of a range of
microvascular disorders as described below.
1. Diabetic Retinopathy
RTP801 promotes neuronal cell apoptosis and generation of reactive oxygen species in vitro.
The inventor of the current invention also found that in RTP801 knockout (KO) mice
subjected to the model of retinopathy of prematurity (ROP), pathologic neovascularization NV
was reduced under hypoxic conditions, despite elevations in VEGF, whereas the lack of this
gene did not influence physiologic neonatal retinal NV. Moreover, in this model, lack of
RTP801 was also protective against hypoxic neuronal apoptosis and hyperoxic vasoobl
iteration.
Experiment 1
Diabetes was induced in 8wk old RTP801 KO and C57/129sv wildtype (WT) littermate mice by
intraperitoneal injection of STZ. After 4 weeks, ERG (single white flash, 1.4xlOA4 ftc, 5 ms)
was obtained from the left eye after 1 hour of dark adaptation.. RVP was assessed from both
eyes using the Evans-blue albumin permeation technique.
Results
Blood glucose was not different between diabetic (DM) WT and DM KO (495±109 vs 513±76
mg/dl), nor nondiabetic (NDM) WT and KO (130±10 vs 135±31 mg/dl, respectively). RVP in
the DM WT group was increased 138% (5\.2± 37.9 uL/g/hr, n=8) compared to NDM WT (21.5
± 18.8 uL/g/hr, n=9, p=0.055). In contrast, RVP was reduced by 80% in DM KO (9.5 ± 8.5
uL/g/hr, n-6, p=0.023) as compared to the DM WT mice, resulting in a 140% decrease of
diabetes-induced RVP. In DM WT mice, there was a prolongation (p potential implicit times for OP2 (11%), OP3 (12%), & OP4 (14%) and for the B-wave (23%) as
compared to NDM WT. A-wave was not significantly changed. These changes were
normalized -100% in DM KO mice for OP3 & OP4 and 65% for B-wave as compared to NDM
KO. Conclusion; Knock out of RTP801 ameliorates diabetes-induced RVP and ERG
abnormalities in mice, suggesting that this hypoxia inducible gene may serve an important role
in the pathogenesis of early diabetic retinal disease.
Experiment 2
Diabetes was induced in RTP801 knockout and in control wild type mice with the matched
genetic background. In addition, it was induced in C57B16 mice, which were subsequently used
for intravitreal injection of anti-RTP801 and control siRNAs. For diabetes induction, the mice
were injected with streptozotocin (STZ 90 mg/kg/d for 2 days after overnight fast). Animal
physiology was monitored throughout the study for changes in blood glucose, body weight, and
hematocrit. Vehicle-injected mice served as controls. The appropriate animals were treated by
intravitreal injections of lug of REDD 14 anti-RTP801 siRNA or lug of anti-GFP control
siRNA. siRNA was injected twice in the course of the study - on day 0, when the first STZ
injection was performed, and on day 14 after the STZ injection.
Retinal vascular leakage was measured using the Evans-blue (EB) dye technique on the animals
after 4 weeks duration of diabetes. Mice had a catheter implanted into the right jugular vein 24
hours prior to Evans Blue (EB) measurements. Retinal permeability measurements in both eyes
of each animal followed a standard Evans-blue protocol.
Results
1. Retinal blood vessel leakage was reduced by 70% in RTP801 KO diabetic mice
compared with wild type diabetic mice (see Figure 20).
2. The Knock out of RTP801 normalizes ERG abnormalities in mice: In DM WT mice,
there was a prolongation (p (11%), OP3 (12%), & OP4 (14%) and for the B-wave (23%) as compared to NDM WT.
A-wave was not significantly changed. These changes were normalized ~100% in DM
RTP801 KO mice for OP3 & OP4 and 65% for B-wave as compared to NDM RTP801
KO (see Figure 21).
3. Similarly to the results in KO mice, retinal blood vessel leakage was reduced by 50% in
diabetic mice injected intravitreally with REDD 14 siRNA against RTP801 compared to
diabetic mice intraviterally injected with control siRNA against GFP (see Figure 22).
2. Retinopathy of prematurity
Retinopathy of prematurity was induced by exposing the test animals to hypoxic and hyperoxic
conditions, and subsequently testing the effects on the retina. Results showed that RTP801 KO
mice were protected from retinopathy of prematurity, thereby validating the protective effect of
RTP801 inhibition.
3. Myocardial infarction
Myocardial infarction was induced by Left Anterior Descending artery ligation in mice, both
short term and long term. Results: reduction of TnT and CPK-MB fraction levels at 24 hrs
postinfarct in the blood and better echocardiogram (ejection fraction volume) at 28 days
postinfarct in RTP801 KO mice.
4. Microvascular Ischemic conditions
Animal models for assessing ischemic conditions include:
1. Closed Head Injury (CHI) - Experimental TBI produces a series of events
contributing to neurological and neurometabolic cascades, which are related to the
degree and extent of behavioral deficits. CHI is induced under anesthesia, while a
weight is allowed to free-fall from a prefixed height (Chen et al, J. Neurotrauma 13,
557, 1996) over the exposed skull covering the left hemisphere in the midcoronal
plane.
2. Transient middle cerebral artery occlusion (MCAO) - a 90 to 120 minutes transient
focal ischemia is performed in adult, male Sprague Dawley rats, 300-370 gr. The
method employed is the intraluminal suture MCAO (Longa et al., Stroke, 30, 84,
1989, and Dogan et al., J. Neurochem. 72, 765, 1999). Briefly, under halothane
anesthesia, a 3-0-nylon suture material coated with Poly-L-Lysine is inserted into the
right internal carotid artery (ICA) through a hole in the external carotid artery. The
nylon thread is pushed into the ICA to the right MCA origin (20-23 mm). 90-120
minutes later the thread is pulled off, the animal is closed and allowed to recover.
3. Permanent middle cerebral artery occlusion (MCAO) - occlusion is permanent,
unilateral-induced by electrocoagulation of MCA. Both methods lead to focal brain ischemia
of the ipsilateral side of the brain cortex leaving the contralateral side intact (control). The
left MCA is exposed via a temporal craniectomy, as described for rats by Tamura A.et al., J
Cereb Blood Flow Metab. 1981;1:53-60. The MCA and its lenticulostriatal branch are
occluded proximally to the medial border of the olfactory tract with microbipolar
coagulation. The wound is sutured, and animals returned to their home cage in a room
warmed at 26°C to 28°C. The temperature of the animals is maintained all the time with an
automatic thermostat.
5. Acute Renal Failure (ARF)
Testing active siRNA for treating ARF may be done using sepsis-induced ARF or ischemiareperfusion-
induced ARF.
1. Sepsis induced ARF
Two predictive animal models of sepsis-induced ARF are described by Miyaji T, Hu X, Yuen
PS, Muramatsu Y, Iyer S, Hewitt SM, Star RA, 2003, Ethyl pyruvate decreases sepsis-induced
acute renal failure and multiple organ damage in aged mice, Kidney Int. Nov;64(5): 1620-31.
These two models are lipopolysaccharide administration and cecal ligation puncture in mice,
preferably in aged mice.
2. Ischemia-reperfusion-induced ARF
This predictive animal model is described by Kelly KJ, Plotkin Z, Vulgamott SL, Dagher PC,
2003 January,. P53 mediates the apoptotic response to GTP depletion after renal ischemiareperfusion:
protective role of a p53 inhibitor, J Am Soc Nephrol.; 14(1): 128-38.
Ischemia-reperfusion injury was induced in rats following 45 minutes bilateral kidney arterial
clamp and subsequent release of the clamp to allow 24 hours of reperfusion. 250 ug of REDD 14
or GFP siRNA (negative control) were injected into the jugular vein 2 hrs prior to and 30
minutes following the clamp. Additional 250ug of siRNA were given via the tail vein at 4 and 8
hrs after the clamp. siRNA against GFP served as a negative control. ARF progression was
monitored by measurement of serum creatinine levels before and 24 hrs post surgery. At the end
of the experiment, the rats were perfused via an indwelling femoral line with warm PBS
followed by 4% paraformaldehyde. The left kidneys were removed and stored in 4%
paraformaldehyde for subsequent histological analysis. Acute renal failure is frequently defined
as an acute increase of the serum creatinine level from baseline. An increase of at least 0.5 mg
per dL or 44.2 umol per L of serum creatinine is considered as an indication for acute renal
failure. Serum creatinine was measured at time zero before the surgery and at 24 hours post
ARF surgery.
To study the distribution of siRNA in the rat kidney, Cy3-labeled 19-mer blunt-ended siRNA
molecules (2 mg/kg) having alternating O-methyl modification in the sugar residues were
administered iv for 3-5 min, after which in vivo imaging was conducted using two-photon
confocal microscopy. The confocal microscopy analysis revealed that the majority of siRNA in
the kidneys is concentrated in the endosomal compartment of proximal tubular cells. Both
endosomal and cytoplasmic siRNA fluorescence were relatively stable during the first 2 hrs post
delivery and disappeared at 24 hrs.
As evident from Figure 19, there was a ten-fold increase in the level of serum creatinine
following a 45-min of kidney bilateral arterial clamp treatment (PBS treatment). Four injections
of 801 siRNA (REDD 14, SEQ In No.s 16 and 66) (2 hrs prior to the clamp and 30min, 4h and
8h after the clamp) significantly reduced the creatinine level in serum by 40% (P results suggest that 801 siRNA can protect renal tissue from the effects of ischemia-reperfusion
injury and thus reduce the severity of ARF.
Example 9
Preparation of siRNAs
Using proprietary algorithms and the known sequence of gene RTP801 (SEQ ID NO:1), the
sequences of many potential siRNAs were generated. siRNA molecules according to the above
specifications were prepared essentially as described herein.
The siRNAs of the present invention can be synthesized by any of the methods which are wellknown
in the art for synthesis of ribonucleic (or deoxyribonucleic) oligonucleotides. For
example, a commercially available machine (available, inter alia, from Applied Biosystems) can
be used; the oligonucleotides are prepared according to the sequences disclosed herein.
Overlapping pairs of chemically synthesized fragments can be ligated using methods well known
in the art (e.g., see U.S. Patent No. 6,121,426). The strands are synthesized separately and then are
annealed to each other in the tube. Then, the double-stranded siRNAs are separated from the
single-stranded oligonucleotides that were not annealed (e.g. because of the excess of one of them)
by HPLC. In relation to the siRNAs or siRNA fragments of the present invention, two or more such
sequences can be synthesized and linked together for use in the present invention.
The siRNA molecules of the invention may be synthesized by procedures known in the art e.g.
the procedures as described in Usman et al., 1987, J. Am. Chem. Soc., 109, 7845; Scaringe et al.,
1990, Nucleic Acids Res., 18, 5433; Wincott et al., 1995, Nucleic Acids Res. 23, 2677-2684;
and Wincott et al., 1997, Methods Mol. Bio., 74, 59, and may make use of common nucleic
acid protecting and coupling groups, such as dimethoxytrityl at the 5'-end, and
phosphoramidites at the 3'-end. The modified (e.g. 2'-0-methylated) nucleotides and
unmodified nucleotides are incorporated as desired.
Alternatively, the nucleic acid molecules of the present invention can be synthesized separately
and joined together post-synthetically, for example, by ligation (Moore et al., 1992, Science 256,
9923; Draper et al., International PCT publication No. W093/23569; Shabarova et al., 1991,
Nucleic Acids Research 19, 4247; Bellon et al., 1997, Nucleosides & Nucleotides, 16, 951;
Bellon et al., 1997, Bioconjugale Chem. 8, 204), or by hybridization following synthesis and/or
deprotection.
The siRNA molecules of the invention can also be synthesized via a tandem synthesis
methodology, as described in US patent application publication No. US2004/0019001
(McSwiggen) wherein both siRNA strands are synthesized as a single contiguous
oligonucleotide fragment or strand separated by a cleavable linker which is subsequently
cleaved to provide separate siRNA fragments or strands that hybridize and permit purification of
the siRNA duplex. The linker can be a polynucleotide linker or a non-nucleotide linker.
For further information, see PCT publication No. WO 2004/015107 (ATUGEN).
As described above, the siRNAs of Table A (below) were constructed such that alternate sugars
have 2'-O-methyl modification i.e. alternate nucleotides were thus modified. In these preferred
embodiments, in one strand of the siRNA the modified nucleotides were numbers
1,3,5,7,9,11,13,15,17 and 19 and in the opposite strand the modified nucleotides were numbers
2,4,6,8,10,12,14,16 and 18. Thus these siRNAs are blunt-ended 19-mer RNA molecules with
alternate 2-0'-methyl modifications as described above. The siRNAs of Tables 2 and 3 (below)
are also constructed in this manner; the siRNAs of Table B are blunt-ended 19-mer RNA
molecules with alternate 2-0'-methyl modifications; the siRNAs of Table C are blunt-ended 21-
mer RNA molecules with alternate 2-0'-methyl modifications.
Table A details various novel siRNA molecules which were generated and subsequently
synthesized for gene RTP801. The two final columns indicate the results of two experiments
performed to examine the activity of the novel molecules. Briefly, HeLa or Hacat cells were
transfected with a specific novel siRNA to be tested. Expression of the RTP801 polypeptide
was then determined by western blotting using an antibody against the RTP801 polypeptide.
Referring to the two right-hand columns of Table A, "-" signifies an inactive or low-activity
molecule (which does not substantially inhibit the expression of the RTP801 gene); "+" signifies
an siRNA molecule with some inhibitory activity (of RTP801 gene expression), "+4-" signifies a
molecule with higher inhibitory activity, and so on. Any one of the the siRNA molecules
disclosed herein, and in particular the active molecules detailed in Table A are novel and also
considered a part of the present invention.
TABLE A
(Table Removed)
Note that in the above Table A, the sense strands of siRNAs 1-50 have SEQ ID NOS: 3-52
respectively, and the antisense strands of siRNAs 1-50 have SEQ ID NOS: 53-102 respectively.
The molecule designated REDD 14 has SEQ ID Nos 16 (Sense strand) and 66 (antisense strand).
TABLES
(Table Removed)
Note that in the above Table B, the sense strands of siRNAs 51-122 have SEQ ID NOS: 103-174
respectively, and the antisense strands of siRNAs 51-122 have SEQ ID NOS: 175-246
respectively.
TABLEC
(Table Removed)
Note that in the above Table C, the sense strands of siRNAs 123-171 have SEQ ID NOS: 247-
295 respectively, and the antisense strands of siRNAs 123-171 have SEQ ID NOS: 296-344
respectively.
Example 10
Pharmacology and drue delivery
The nucleotide sequences of the present invention can be delivered either directly or with viral
or non-viral vectors. When delivered directly the sequences are generally rendered nuclease
resistant. Alternatively the sequences can be incorporated into expression cassettes or constructs
such that the sequence is expressed in the cell as discussed herein below. Generally the construct
contains the proper regulatory sequence or promoter to allow the sequence to be expressed in
the targeted cell.
The compounds or pharmaceutical compositions of the present invention are administered and
dosed in accordance with good medical practice, taking into account the clinical condition of the
individual patient, the disease to be treated, the site and method of administration, scheduling of
administration, patient age, sex, body weight and other factors known to medical practitioners.
The pharmaceutically "effective amount" for purposes herein is thus determined by such
considerations as are known in the art. The amount must be effective to achieve improvement
including but not limited to improved survival rate or more rapid recovery, or improvement or
elimination of symptoms and other indicators as are selected as appropriate measures by those
skilled in the art.
The treatment generally has a length proportional to the length of the disease process and drug
effectiveness and the patient species being treated. It is noted that humans are treated generally
longer than the mice or other experimental animals exemplified herein.
The compounds of the present invention can be administered by any of the conventional routes
of administration. It should be noted that the compound can be administered as the compound or
as pharmaceutically acceptable salt and can be administered alone or as an active ingredient in

combination with pharmaceutically acceptable carriers, solvents, diluents, excipients, adjuvants
and vehicles. The compounds can be administered orally, subcutaneously or parenterally
including intravenous, intraarterial, intramuscular, intraperitoneally, and intranasal
administration as well as intrathecal and infusion techniques. Implants of the compounds are
also useful. Liquid forms may be prepared for injection, the term including subcutaneous,
transdermal, intravenous, intramuscular, intrathecal, and other parental routes of administration.
The liquid compositions include aqueous solutions, with and without organic cosolvents,
aqueous or oil suspensions, emulsions with edible oils, as well as similar pharmaceutical
vehicles. In addition, under certain circumstances the compositions for use in the novel
treatments of the present invention may be formed as aerosols, for intranasal and like
administration. The patient being treated is a warm-blooded animal and, in particular, mammals
including man. The pharmaceutically acceptable carriers, solvents, diluents, excipients,
adjuvants and vehicles as well as implant carriers generally refer to inert, non-toxic solid or
liquid fillers, diluents or encapsulating material not reacting with the active ingredients of the
invention.
When administering the compound of the present invention parenterally, it is generally
formulated in a unit dosage injectable form (solution, suspension, emulsion). The
pharmaceutical formulations suitable for injection include sterile aqueous solutions or
dispersions and sterile powders for reconstitution into sterile injectable solutions or dispersions.
The carrier can be a solvent or dispersing medium containing, for example, water, ethanol,
polyol (for example, glycerol, propylene glycol, liquid polyethylene glycol, and the like),
suitable mixtures thereof, and vegetable oils.
Proper fluidity can be maintained, for example, by the use of a coating such as lecithin, by the
maintenance of the required particle size in the case of dispersion and by the use of surfactants.
Nonaqueous vehicles such a cottonseed oil, sesame oil, olive oil, soybean oil, com oil,
sunflower oil, or peanut oil and esters, such as isopropyl myristate, can also be used as solvent
systems for compound compositions. Additionally, various additives which enhance the
stability, sterility, and isotonicity of the compositions, including antimicrobial preservatives,
antioxidants, chelating agents, and buffers, can be added. Prevention of the action of
microorganisms can be ensured by various antibacterial and antifungal agents, for example,
parabens, chlorobutanol, phenol, sorbic acid, and the like. In many cases, it is desirable to
include isotonic agents, for example, sugars, sodium chloride, and the like. Prolonged
absorption of the injectable pharmaceutical form can be brought about by the use of agents
delaying absorption, for example, aluminum monostearate and gelatin. According to the present
invention, however, any vehicle, diluent, or additive used have to be compatible with the
compounds.
Sterile injectable solutions can be prepared by incorporating the compounds utilized in
practicing the present invention in the required amount of the appropriate solvent with various
of the other ingredients, as desired.
A pharmacological formulation of the present invention can be administered to the patient in an
injectable formulation containing any compatible carrier, such as various vehicle, adjuvants,
additives, and diluents; or the compounds utilized in the present invention can be administered
parenterally to the patient in the form of slow-release subcutaneous implants or targeted delivery
systems such as monoclonal antibodies, vectored delivery, iontophoretic, polymer matrices,
liposomes, and microspheres. Examples of delivery systems useful in the present invention
include U. S. Patent Nos. 5,225,182; 5,169,383; 5,167,616; 4,959,217; 4,925,678; 4,487,603;
4,486,194; 4,447,233; 4,447,224; 4,439,196; and 4,475,196. Many other such implants, delivery
systems, and modules are well known to those skilled in the art.
A pharmacological formulation of the compound utilized in the present invention can be
administered orally to the patient. Conventional methods such as administering the compound in
tablets, suspensions, solutions, emulsions, capsules, powders, syrups and the like are usable.
Known techniques which deliver it orally or intravenously and retain the biological activity are
preferred. In one embodiment, the compound of the present invention can be administered
initially by intravenous injection to bring blood levels to a suitable level. The patient's levels are
then maintained by an oral dosage form, although other forms of administration, dependent
upon the patient's condition and as indicated above, can be used.
In general, the active dose of compound for humans is in the range of from Ing/kg to about 20-
100 mg/kg body weight per day, preferably about 0.01 mg to about 2-10 mg/kg body weight per
day, in a regimen of one dose per day or twice or three or more times per day for a period of 1 -2
weeks or longer, preferably for 24-to 48 hrs or by continuous infusion during a period of 1-2
weeks or longer.
Administration of compounds of the present invention to the eve
The compounds of the present invention can be administered to the eye topically or in the form
of an injection, such as an intravitreal injection, a sub-retinal injection or a bilateral injection.
Further information on administration of the compounds of the present invention can be found
in Tolentino et al., Retina 24 (2004) 132-138; Reich et al., Molecular vision 9 (2003) 210-216.
Pulmonary administration of compounds of the present invention
The therapeutic compositions of the present invention are preferably administered into the lung
by inhalation of an aerosol containing these compositions / compounds, or by intranasal or
intratracheal instillation of said compositions. Formulating the compositions in liposomes may
benefit absorption. Additionally, the compositions may include a PFC liquid such as perflubron,
and the compositions may be formulated as a complex of the compounds of the invention with
polyethylemeimine (PEI).
For further information on pulmonary delivery of pharmaceutical compositions see Weiss et al.,
Human gene therapy 10:2287-2293 (1999); Densmore et al., Molecular therapy 1:180-188
(1999); Gautam et al., Molecular therapy 3:551-556 (2001); and Shahiwala & Misra, AAPS
PharmSciTech 5 (2004). Additionally, respiratory formulations for siRNA are described in U.S.
patent application No. 2004/0063654 of Davis et el.
Additional formulations for improved delivery of the compounds of the present invention can
include non-formulated compounds, compounds covalently bound to cholesterol, and
compounds bound to targeting antibodies (Song et al., Antibody mediated in vivo delivery of
small interfering RNAs via cell-surface receptors, Nat Biotechnol. 2005 Jun;23(6):709-17).






We Claim:
1. A compound having the double-stranded structure:
(Formula Removed)
wherein each N and N' is a ribonucleotide which may be modified or unmodified in its sugar residue and each of (N)x and (N')y is an oligomer in which each consecutive N or N' is joined to the next N or N' by a covalent bond;
wherein each of x and y is an integer between 19 and 40 inclusive;
wherein each of Z and Z' may be present or absent, but if present is dTdT and is covalently attached at the 3' terminus of the strand in which it is present;
and wherein the sequence of (N)x comprises a first stretch of contiguous nucleotides having any one of the following sequences:
AGCUGCAUCAGGUUGGCAC (SEQ ID NO:66); UUCUAGAUGGAAGACCCAG (SEQ ID NO:74); UUGAACAUCAAGUGUAUUC (SEQ ID NO:75); AAAAAUAUUGCAUAGGUCU (SEQ ID NO:77); UACUUGAACAUCAAGUGUA (SEQ ID NO:79); and AACUCAAUGAGCUUCCUGG (SEQ ID NO:91);
and the sequence of (N')y comprises a second stretch of contiguous nucleotides,
and wherein the double-stranded structure is generated by base-pairing between the first stretch and the second stretch.
2. A compound as claimed in claim 1, wherein a sugar residue in at least one ribonucleotide is modified.
3. A compound as claimed in claim 2, wherein the sugar residue is modified by replacing an -OH at the 2' position with -H, -OCH3, -OCH2CH3, -OCH2CH2CH3, -NH2, or -F.

4. A compound as claimed in claim 3, wherein the -OH is replaced with -OCH3.
5. A compound as claimed in claim 4, wherein the covalent bond is a phosphodiester bond; x = y, preferably x = y = 19; Z and Z' are both absent; alternating ribonucleotides in each of the antisense and the sense strands comprise a 2'-OCH3 modification in their sugar residues; and the ribonucleotides at the 5' and 3' termini of the antisense strand are so modified and the ribonucleotides at the 5' and 3' termini of the sense strand are unmodified.
6. A compound as claimed in any one of claims 1-6, wherein x = y = 19.
7. A compound as claimed in any one of claims 1-6, wherein the compound is phosphorylated or non-phosphorylated.
8. A compound as claimed in any one of claims 1-4 and 6-7, wherein the dinucleotide dTdT is covalently attached to the 3' terminus of the antisense strand or the sense strand.
9. A compound as claimed in any one of claims 1-8, wherein the sequence of (N)x comprises the following sequence: AGCUGCAUCAGGUUGGCAC (SEQ ID NO:66).
10. A compound as claimed in any one of claims 1 -7 and 9 having the structure:
5' AGCUGCAUCAGGUUGGCAC 3' antisense strand (SEQ ID NO:66)
3' UCGACGUAGUCCAACCGUG 5' sense strand (SEQ ID NO: 16)
wherein alternating ribonucleotides in the antisense and the sense strands comprise a 2'-OCH3 modification in the sugar residue of the ribonucleotides; the ribonucleotides at the 5' and 3' termini of the antisense strand comprise the 2'-OCH3 modification; the ribonucleotides at the 5' and 3' termini of the sense strand are unmodified; the ribonucleotide at each of the 5' terminus and the 3' terminus of the antisense strand and the sense strand is independently phosphorylated or non-phosphorylated; and each vertical line represents base pairing between the ribonucleotides.

11. A compound as claimed in claim 10 wherein both the antisense and the sense strands are non-phosphorylated at the 3' termini or the 3' and 5' termini.
12. A compound as claimed in claim 10 wherein both the antisense and the sense strands are phosphorylated at the 3' and 5' termini.
13. A pharmaceutical composition comprising a compound as claimed in any one of claims 1-12 at a range of from 1ng/kg to about 20-100ng/kg body weight.
14. The composition as claimed in claim 13 wherein the compound has one of the following structures:
5' AGCUGCAUCAGGUUGGCAC 3' antisense strand (SEQ ID NO:66)
3' UCGACGUAGUCCAACCGUG 5' sense strand (SEQ ID NO: 16)
wherein alternating ribonucleotides in the antisense and the sense strands comprise a 2'-0-methyl modification in the sugar residue of the ribonucleotides; wherein the ribonucleotides at the 5' and 3' termini of the antisense strand comprise the 2'-0-methyl modification; wherein the ribonucleotides at the 5' and 3' termini of the sense strand are unmodified; and wherein the antisense and the sense strands are non-phosphorylated at the 3' termini; or
5' AGCUGCAUCAGGUUGGCAC 3' antisense strand (SEQ ID NO:66)
3' UCGACGUAGUCCAACCGUG 5' sense strand (SEQ ID NO: 16)
wherein alternating ribonucleotides in the antisense and the sense strands comprise a 2'-0-methyl modification in the sugar residue of the ribonucleotides; wherein the ribonucleotides at the 5' and 3' termini of the antisense strand comprise the 2'-0-methyl modification; wherein the ribonucleotides at the 5' and 3' termini of the sense strand are unmodified; and wherein the antisense and the sense strands are non-phosphorylated at the 3' and 5' termini; or
5' AGCUGCAUCAGGUUGGCAC 3' antisense strand (SEQ ID N0:66)

3' UCGACGUAGUCCAACCGUG 5' sense strand (SEQ ID NO: 16)
wherein alternating ribonucleotides in the antisense and the sense strands comprise a 2'-0-methyl modification in the sugar residue of the ribonucleotides; wherein the ribonucleotides at the 5' and 3' termini of the antisense strand comprise the 2'-0-methyl modification; wherein the ribonucleotides at the 5' and 3' termini of the sense strand are unmodified; and wherein the antisense and the sense strands are phosphorylated at the 3' and 5' termini.
15. The compound as claimed in any one of claims 1-12 or the composition according to claim 13 or 14 for use in treating a respiratory disorder, an eye disease, a microvascular disorder or a spinal cord injury or disease.
16. The compound as claimed in claim 15, for use in treating an eye disease.
17. The compound as claimed in claim 16, wherein the eye disease is glaucoma.
18. The compound as claimed in claim 16, wherein the eye disease is macular degeneration.
19. The compound as claimed in claim 18, wherein the eye disease is age-related macular degeneration (AMD).
20. The compound as claimed in claim 19, wherein the age-related macular degeneration (AMD) is wet AMD.
21. The compound as claimed in claim 16, wherein the eye disease is secondary to diabetes.
22. The compound as claimed in claim 21, wherein the eye disease is diabetic retinopathy.
23. The compound as claimed in claim 21, wherein the eye disease is diabetic macular edema (DME).

24. The compound as claimed in claim 15, for use in treating a microvascular disorder.
25. The compound as claimed in claim 24, wherein the microvascular disorder is acute renal failure (ARF).
26. The compound as claimed in claim 15, for use in treating a respiratory disorder.
27. The compound as claimed in claim 26, wherein the respiratory disorder is chronic obstructive pulmonary disease (COPD).
28. The compound as claimed in claim 26, wherein the respiratory disorder is asthma.
29. The compound as claimed in claim 26, wherein the respiratory disorder is emphysema.
30. The compound as claimed in claim 26, wherein the respiratory disorder is chronic bronchitis.

Documents:

1967-DELNP-2007-Abstract-(08-07-2011).pdf

1967-delnp-2007-abstract.pdf

1967-DELNP-2007-Claims-(08-07-2011).pdf

1967-DELNP-2007-Claims-(15-10-2008).pdf

1967-delnp-2007-Claims-(19-09-2013).pdf

1967-DELNP-2007-Claims-(25-06-2009).pdf

1967-delnp-2007-claims.pdf

1967-DELNP-2007-Correspodence Others-(08-07-2011).pdf

1967-DELNP-2007-Correspondence Others-(15-06-2012).pdf

1967-DELNP-2007-Correspondence Others-(18-07-2011).pdf

1967-delnp-2007-Correspondence Others-(19-09-2013).pdf

1967-delnp-2007-Correspondence Others-(29-05-2012).pdf

1967-DELNP-2007-Correspondence-Others-(15-10-2008).pdf

1967-DELNP-2007-Correspondence-Others-(16-06-2009).pdf

1967-DELNP-2007-Correspondence-Others-(23-02-2010).pdf

1967-DELNP-2007-Correspondence-Others-(25-06-2009).pdf

1967-delnp-2007-correspondence-others-1.pdf

1967-delnp-2007-correspondence-others.pdf

1967-DELNP-2007-Description (Complete)-(08-07-2011).pdf

1967-delnp-2007-description (complete).pdf

1967-DELNP-2007-Drawings-(08-07-2011).pdf

1967-delnp-2007-drawings.pdf

1967-DELNP-2007-Form-1-(08-07-2011).pdf

1967-delnp-2007-form-1.pdf

1967-DELNP-2007-Form-13-(08-07-2011).pdf

1967-delnp-2007-form-13-(15-10-2008).pdf

1967-delnp-2007-form-13-(16-06-2009).pdf

1967-delnp-2007-form-13-(25-06-2009).pdf

1967-delnp-2007-form-18.pdf

1967-DELNP-2007-Form-2-(08-07-2011).pdf

1967-delnp-2007-form-2.pdf

1967-DELNP-2007-Form-3-(08-07-2011).pdf

1967-delnp-2007-Form-3-(29-05-2012).pdf

1967-delnp-2007-form-3.pdf

1967-delnp-2007-form-5.pdf

1967-DELNP-2007-GPA-(08-07-2011).pdf

1967-DELNP-2007-Others-Document-(15-10-2008).pdf

1967-DELNP-2007-Others-Documents-(16-06-2009).pdf

1967-delnp-2007-pct-101.pdf

1967-delnp-2007-pct-306.pdf

1967-DELNP-2007-Petition 137-(08-07-2011).pdf

1967-delnp-2007-ur-Claims-(19-09-2013).pdf


Patent Number 258358
Indian Patent Application Number 1967/DELNP/2007
PG Journal Number 01/2014
Publication Date 03-Jan-2014
Grant Date 02-Jan-2014
Date of Filing 14-Mar-2007
Name of Patentee QUARK PHARMACEUTICALS, INC.
Applicant Address 6501 DUMBARTON CIRCLE, FREMONT, CA 94555, UNITED STATES OF AMERICA.
Inventors:
# Inventor's Name Inventor's Address
1 KLAUS GIESE AND JORG KAUFMANN C/O ATUGEN AG, ROBERT-ROSSLE-STR.10, 13125 BERLIN,GERMANY
2 ELENA FEINSTEIN 12/29 HAHAGANA STREET, REHOVOT, ISRAEL
3 KLAUS GIESE AND JORG KAUFMANN C/O ATUGEN AG, ROBERT-ROSSLE-STR.10, 13125 BERLIN,GERMANY
4 ELENA FEINSTEIN 12/29 HAHAGANA STREET, REHOVOT, ISRAEL
PCT International Classification Number A61K 48/00
PCT International Application Number PCT/US2005/029236
PCT International Filing date 2005-08-16
PCT Conventions:
# PCT Application Number Date of Convention Priority Country
1 60/601,983 2004-08-17 U.S.A.
2 60/688,943 2005-06-08 U.S.A.
3 60/604,668 2004-08-25 U.S.A.
4 60/638,659 2004-12-22 U.S.A.
5 60/609,786 2004-09-14 U.S.A.